safc supply solutions - proligo® reagents catalog

Proligo® Reagents Nucleic acid solutions for genomic developmentPhosphoramidites / Modifiers / Supports / Liquid Reagents

Welcome to the future of genomics

www.safcsupplysolutions.com

SAFC International SitesGlobal E-mail: [email protected]

ArgentinaTel: +54 11 4556 1472Fax: +54 11 4552 1698E-Mail: [email protected]

AustraliaFree Tel: 1800 800 097 Free Fax: 1800 800 096Tel: +61 (0)2 9841 0555Fax: +61 (0)2 9841 0500E-Mail: [email protected]

AustriaTel: +43 (0)1 605 81 91 Fax: +43 (0)1 605 81 20E-Mail: [email protected]

BelgiumFree Tel: 0800 99560Free Fax: 0800 99561 Tel: +31 78 6205414Fax: +31 78 6205424E-Mail: [email protected]

BrazilTel: +55 11 3732 3100Fax: +55 11 3733 5151E-Mail: [email protected]

CanadaFree Tel: 1800 565 1400Free Fax: 1800 265 3858Tel: +1 905 829 9500Fax: +1 905 829 9292E-Mail: [email protected]

ChinaTel: +86 21 6386 2766Fax: +86 21 6386 3966E-Mail: [email protected]

Czech RepublicTel: +420 246 003 200Fax: +420 246 003 291E-Mail: [email protected]

DenmarkTel: +45 43 565 900 Fax: +45 43 565 905E-Mail: [email protected]

FinlandTel: +358 9 350 9250Fax: +358 9 350 92555E-Mail: [email protected]

FranceTel: +33 (0)4 74 82 2882Fax: +33 (0)4 74 82 2890E-Mail: [email protected]

GermanyTel: +49 (0)89 6513 1920Fax: +49 (0)89 6513 1919E-Mail: [email protected]

GreeceTel: +30 2 10 994 8010Fax: +30 2 10 994 3831E-Mail: [email protected]

HungaryTel: +36 (06) 1 235 9066 Fax: +36 (06) 1 235 9050Ingyenes zöldtelefon: 06 80 355 355Ingyenes zöld fax: 06 80 344 344E-Mail: [email protected]

IndiaBangaloreTel: +91 80 5112 7272Fax: +91 80 5112 7473New Delhi Tel: +91 11 2616 5477Fax: +91 11 2616 5611Mumbai Tel: +91 22 2570 2364Fax: +91 22 2579 7589Hyderabad Tel: +91 40 5531 5488Fax: +91 40 5531 5466E-Mail: [email protected]

IrelandTel: +353 (0)1 404 1903 Fax: +353 (0)1 404 1911E-Mail: [email protected]

IsraelFree Tel: +1 800 70 2222 Tel: +972 8 948 4100 Fax: +972 8 948 4200 E-Mail: [email protected]

ItalyTelefono: +39 02 3341 7350Fax: +39 02 3341 7201E-Mail: [email protected]

JapanTel: +81 (0)3 5796 7340Fax: +81 (0)3 5796 7345E-Mail: [email protected]

KoreaTel: +82 (0)31 329 9000Fax: +82 (0)31 329 9090E-Mail: [email protected]

MalaysiaTel: +60 3 5635 3321Fax: +60 3 5635 4116E-Mail: [email protected]

MexicoFree Tel: 01 800 007 5300Free Fax: 01 800 712 9920E-Mail: [email protected]

The NetherlandsTel: +31 (0)78 620 5414Fax: +31 (0)78 620 5424Free Tel: 0800 022 9092Free Fax: 0800 022 9093E-Mail: [email protected]

New ZealandFree Tel: 0800 936 666Free Fax: 0800 937 777

NorwayTel: +47 (0)23 176 000Fax: +47 (0)23 176 010E-Mail: [email protected]

PolandTel: +48 61 829 0100Fax: +48 61 829 0120E-Mail: [email protected]

PortugalTel: +351 21 924 25 55Fax: +351 21 924 26 10Free Tel: 800 20 21 80Free Fax: 800 20 21 78E-Mail: [email protected]

RussiaTel: +7 495 975 3321Fax: +7 495 975 4792E-Mail: [email protected]

SingaporeTel: +65 6779 1200Fax: +65 6779 1822E-Mail: [email protected]

South AfricaFree Tel: 0800 1100 75Free Fax: 0800 1100 79Tel: +27 11 979 1188Fax: +27 11 979 1119E-Mail: [email protected]

SpainTel: +34 91 657 2073 Fax: +34 91 490 5785 E-Mail: [email protected]

SwedenTel: +46 (0)8 742 4200 Fax: +46 (0)8 742 4243E-Mail: [email protected]

SwitzerlandSwiss Free Call: 0800 80 00 80Tel: +41 (0) 81 755 27 32Fax: +41 (0) 81 755 27 70E-Mail: [email protected]

United KingdomPooleTel: +44 (0)1202 712 305Fax: +44 (0)1202 712 235GillinghamTel: +44 (0)1202 712305Fax: +44 (0)1202 712235ManchesterTel: +44 (0)161 232 5500Fax: +44 (0)161 232 5501E-Mail: [email protected]

United StatesToll Free: 800 244 1173Call Collect: 314 534 4900Toll Free Fax: 800 368 4661Fax: 314 652 0000E-Mail: [email protected]

SAFC Proligo® ReagentsGeorg-Heyken Str.1421147 HamburgGermanyTel: +49 407 970 2250Fax: +49 407 970 2100E-Mail: [email protected]


KMI043530408

SAFC Supply Solutions®, Pharmadite®, SAFC Proligo® Reagents, andActivator 42® are a registered trademarks of Sigma-Aldrich

Biotechnology L.P. and Sigma-Aldrich Co.

Millipore® and CPG® are U.S. registered trademarks owned by MilliporeCorporation or an affiliated company.

Perkin-Elmer® and Perseptive Biosystems® are registered trademarks ofthe Perkin-Elmer Corporation, PerSeptive Biosystems, Inc. or other

subsidiaries in the U.S. and certain other countries.

ABI® is a registered trademark of Applera Corporation or its subsidiaries.

Expedite™ is a trademark of Applera Corporation or its subsidiaries.

PolyGen® is a registered trademark of PolyGen GmbH.

*LNA® / Locked Nucleic Acid® is a registered trademark of Exiqon A/S, Vedbaek, Denmark.

Cy trademarks are licensed through Molecular Probes which is now fully owned by Invitrogen.

All other trademarks are the property of their respective owners.Reproduction forbidden without permission.

LNA oligonucleotides and phosphoramidites are sold under license from Exiqon A/S for research use only. Not for resale or for therapeutic

use or use in humans. Specifications are subject to change.

© 2008 SAFC All rights reservedPrinted in USA

http://www.sigma-aldrich.com?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

http://www.safcsupplysolutions.com?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf


http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

Strength In Our HistoryOur beginnings are aligned with theinfancy of nucleic acid synthesistechnologies. In 1981, Professor HubertKöster founded Biosyntech GmbH,incorporating proprietary nucleic acidsynthesis technologies in Hamburg,Germany. Since that time, the entireindustry has undergone numeroustransformations, and our nucleic acidchemistry expertise and manufacturingcapabilities have remained at its forefront.

Today, Proligo® Reagents from SAFCSupply Solutions® are recognized theworld over for their quality. Our historyof providing DNA and RNA synthesisreagents and supporting services is onecustomers have depended upon in theiroglionucleotide programs for over 27 years.

SAFC Supply Solutions®



SAFC Supply Solutions® recognizes that, as products move through pharmaceutical and diagnostic development, technologies and compliance requirements evolve.

With over 25 years of experience in our Hamburg manufacturing facility, we bring you Proligo® Reagents, a dedicated and comprehensive line of raw materials for oligonucleotides synthesis including DNA and RNA Pharmadites, standard and modified Amidites, Linkers & Modifiers, Supports & Solvents.

Contact your local representative to learn more about our technical and quality package.

To be inspiredmeet us at theyearly TIDESshow (US)

1981 Biosyntech GmbH proprietarynucleic acid synthesistechnologies founded byProfessor Hubert Köster

1986 Biosyntech acquired by Milligen,a division of Millipore®, Inc.

1991 Transfer of Biosearch chemicaloperations from California toHamburg, Germany

1993 First ISO 9001 biotechnologycompany certified in Germany

1994 Integration into PerSeptiveBiosytems®, Inc.

1995 Acquisition of Controlled PoreGlass (CPG®) technology

1996 Manufacturing facilitiesimproved to state-of-the-art

1998 PerSeptive Biosystems®, Inc.merges with Perkin-Elmer®

Corporation

1998 Proligo® Reagents founded bySKW and NeXstar

2002 Proligo® Reagents multi-tonmanufacturing capabilitiesintroduced

2005 Proligo® Reagents purchased bySigma-Aldrich, Inc. for its SAFC®

custom manufacturing group

To place an order or inquire aboutcustom manufacturing contact yourlocal SAFC representative or visitwww.safcsupplysolutions.com

1

Table of Contents

SAFC Supply Solutions® Proligo® Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Manufacturing, Purification & Filling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Custom Manufacturing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Quality Assurance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Packaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Pharmadite® for Pharmaceutical Applications . . . . . . . . . . . . . . . . . . . . . . . . . 8

DNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Fast Deprotection Chemistries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

2'O-Methyl RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

DMT-2'Fluoro Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Labels and Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Non-Standard Nucleosides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Phosphate-ON Phosphoramidite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

NPPOC Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Solid Supports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Controlled Pore Glass and Columns — CPG Free Flow . . . . . . . . . . . . . . . . 42

Columns for Synthesizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Amino-ON CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Universal CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Liquid Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Activator 42® . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Product List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Manufacturing

Phosphoramidites and controlled pore glass (CPG)solid supports are produced in our state-of-the-artHamburg, Germany manufacturing facilities. To servethe global market, standard formulation and customrequests for liquid formulations, solvents and reagentsare produced in explosion-proof environments at theHamburg site and at our Sheboygan, Wisconsinmanufacturing facility in the U.S.

Because we are a leading manufacturer, SAFCSupply Solutions has the flexibility to supply a widevariety of high-volume standard products as wellas manufacture small-scale custom specialties.Dedicated labs and extensive processdevelopment and scale-up expertise complimentsour multiple production suites while our largecapacity ensures quick response time to satisfyever-changing market demands.

Flexible production comes from numerous mid-size reactor trains (20-200L), glass-lined reactors to1,000L, temperature ranges from -30ºC to 160ºC,and an integrated solvent delivery system.

HPLC Purification

DNA and RNA phosphoramidites are our specialty.We purify by preparative column chromatography onsilica gel with medium to high press chromatographyequipment. All materials undergo complete analyticalsupport prior to their release with purificationsupported by:

• Annual amidite purification capacity of over5,000 kg

• Large automated preparative HPLC with scalesto 500 mm column diameter

• DCM handling capability

• Automated batch processing

• State-of-the-art process visualization

• Built-in Clean In Place (CIP) procedures

Filling

Customers appreciate our flexible packagingoptions and we can meet specific requirements forcommercial synthesizers. In liquid fill, our completelysegregated operations support glass bottle anddrum containers. Automated powder fill lines includesynthesis column assembly and custom packaging— from milligrams to tons. Our comprehensiveservices include global warehousing and storagefor our customer’s manufactured products.

Manufacturing, Purification& Filling

The Industry Leader inManufacturing Amiditesand Pharmidites®

A world-class provider of high-purity, high-yield

nucleic acid solutions, SAFC Supply Solutions’

Proligo® Reagents brings revolutionary

innovation and the reliability of outstanding

regulatory compliance to diagnostics and

pharmaceutical customers worldwide involved

in genetic development programs.

Our dedicated experts have extensive experiencemanufacturing key high performance raw materialsfor DNA and RNA oglionucleotide synthesis fordiagnostics and pharmaceutical applications. As thelargest manufacturer of amidites and pharmidites inthe industry, Proligo Reagents’ extensive inventory ofstandard building blocks and custom manufacturingcapabilities can meet the most demandingrequirements. Our product range begins with high-quality starting materials and includes:

• HPLC-purified DNA & RNA phosphoramiditemonomers to ensure consistent quality

• Solvents (manufactured in the U.S. and inHamburg, Germany) that increase yieldthrough extremely low controlled water contentand unique formulations

• Complete scale-up, process development andanalytical method development services

• Complete control and documentation processes

• A highly-qualified scientific staff with extensivebackgrounds in nucleic acid products andspecialty monomers

• An ISO certified manufacturing facility built foramidites production backed by a solid audittrack record

• Phosphoramidite manufacturing capacity ofover 5 tons per year

• The dependability that your intellectual propertywill be treated with respect

2


Proligo® Reagents


3

Custom Manufacturing

SAFC Supply Solutions’ Proligo Reagents is

a skilled custom synthesis manufacturer for

nucleic acids products. Our strong history in

the genomics industry and solid manufacturing

foundation combine with SAFC Supply Solutions’

industry-leading regulatory knowledge and

allows us to manufacture materials to the highest

quality levels demanded by the pharmaceutical

and diagnostics industries.

If you are looking for a unique modifier, you canremain confident our staff has the expertise tosupport your program development, scale-up,analytical, quality assurance, packaging anddistribution, and will never compromise yourintellectual property. We understand the efficienciesgained by proper project management. We realizethe value working with a knowledgeable partnerbrings to every step of process development andwe know the importance of quality assurance. Weunderstand the science and have the capabilities tosupport your cGMP synthesis operations. SAFCSupply Solutions Proligo Reagents is the industry’sleading specialist in manufacturing:

Process/Technology Features Reactions/Examples

Phosphoramidation Introduction of the diisopropyl-β-cyanoethyl

phosphoramidite group

R O P

N

O

C

N

R O H

Tritylation (Dimethoxytritylation) Introduction of triphenylmethyl protective groups

R O C

O C H 3

O C H 3R O H

Silylation/Desilylation Introduction or removal of silyl protective groups Base

O

O O H

O

S i

S i

O

BaseO

H O O H

H O

N- and O-Acylation Introduction of nucleobase and ribose protective groups

N

NO

N H 2

R i b o s e

N

NO

N H

R i b o s e

C

R

O

Nucleobase Conversion Transformation of easily assessable nucleosides to

nucleosides with other nucleobases H N

NO

O

S u g a r

C H 3N

NO

N H 2

S u g a r

C H 3

Preparative Chromatography High-pressure, fully automated separation on normal phase

silica gel including freely programmable gradient elution

Surface Chemistry Loading and capping of functionalized glass and organic

polymer surfaces

N

H

O

O

O

B a s eO

OR

N H 2

>99% purity

• Nucleoside phosphoramidites and otheractivated monomers, nucleobase modifications,non-natural nucleosides, alternative protectivegroups, backbone modifications

• Solid phase synthesis supports loaded withunusual base; alternative linkage

• Modifiers and specialties

• Solutions and solvents for DNA/RNAsynthesizers

SAFC handles these critical materialsfor large-scale production

• Phosphorous trichloride and organicphosphorous (III) chlorides

• Phosphorous oxychloride

• Carbonic acid chlorides

• Trimethylchlorosilane

• Trimethylsilyl triflate

• Dimethylamine

SAFC Capabilities

4


Proligo® Reagents

ComplianceStrong ties in supplying materials to thepharmaceutical industry have helped ourcustomers around the world to understandcompliance requirements of their new materials.Our strict quality control procedures include fulltraceability, complete documentation and changecontrol notification. All our manufacturingprocesses are monitored and reviewed, withcontrols in place at each critical parameter toensure compliance.

Quality ControlSAFC has rigorous QC protocol for every productwe produce to identify purity levels against setspecifications. We can provide custom QC testingupon request. We routinely use these state-of-the-art analytical methods:

• RP & SAX HPLC

• LC-MS

• NMR (31P, 1H, 13C, 19F)

• Nucleic acid synthesis test

• FT-IR

• Titration & “Wet Chemistry”

• UV/VIS

• Karl Fischer water analysis

• Mercury porosimetry

Quality Assurance As a trusted partner to the oglionucloetide market,SAFC assists its customers in new productdevelopment. We know that developing materialsincludes having insight to their qualityrequirements. As a result, our company operatesin a culture that fosters continuous processimprovement and has quality systems in place toprovide complete traceability on all our rawmaterials, processes and procedures. We servecustomers requesting audits with completedocumentation and files. Our quality assurancedepartment routinely accepts requests fordocumentation, including Certificates of Origin.Our Hamburg facility was one of the first in theindustry to be ISO 9001 certified (1993), and wehave synthesized amidites under ISO9000:2000since that time.


5

Standard Bottles and Characteristics

Description Height (cm) Diameter (cm) Quantity (powder) Quantity (liquid reagents)

15 ml septum 4.5 2.9 0.25 g, 0.5 g, 1 g

60 ml septum 10.0 3.3 1 g, 2 g, 4 g

100 ml septum 9.5 5.1 5 g, 10 g 100 ml

1 oz 20/400 (30 ml) 7.8 3.1 0.25 g, 0.5 g, 1 g

2 oz 20/400 (60 ml) 9.4 3.8 1 g, 2 g

8 oz 24/400 (240 ml) 13.7 6.0 10 g 180 ml, 200 ml

8 oz 28/400 (240 ml) 13.7 6.0 5 g, 10 g 200 ml

16 oz 28/400 (480 ml) 17.0 7.2 10 g, 20 g 450 ml

1 g CPG bottle (10 ml) 5.8 2.5 1 g

10 g CPG bottle (50 ml) 9.5 4.0 10 g

V-Vial 20/400 6.0 2.0 0.1 g, 0.25 g

2.5 L GL45 29.6 13.5 2500 ml

4 L 38/430 35.3 16.1 4000 ml

Packaging

15 ml septum 60 ml septum 100 ml septum 1 oz 20/400 2 oz 20/400

8 oz 24/400 8 oz 28/400 16 oz 28/400 1 g CPG 10 g CPG

V-Vial 20/400 2.5 L GL45 4 L 38/430 Bulk Packaging

Flexible packaging options are available to meetvirtually any synthesizer requirement, includingABI® 394, ABI® 3900, Expedite™, AKTA and Mermade.Inquire for custom packaging requirements.

To complete the single-source supplier advantage,from product order to delivery, SAFC has liquidfilling and blending capabilities at its Hamburg and

Sheboygan, Wisconsin facilities with capabilitiesfrom bottles to 1,400 L returnable cylinders. Wehave distribution offices around to globe to offerour customers the convenience of a worldwidedistribution network with the advantages ofdedicated airfreight space, chemical transportregulations and local delivery knowledge.

6


Proligo® Reagents

Standard drums and characteristics

Description Capacity Total Capacity Weight Height Diameter Wall thickness

1400 L Returnable Container 1400 L 1500 L 247 kg 1960 mm 1200 mm N/A

200 L Returnable Drum, Standard 200 L 225 L 43 kg 970 mm 600 mm 2 mm

200 L Returnable Drum, Level Sensor 200 L 225 L 43 kg 970 mm 600 mm 2 mm

200 L Drum, Disposal 180 L 200 L 21 kg 884 mm 585 mm 1 mm

50 L Returnable Drum 45 L 50 L 12 kg 600 mm 363 mm 1.5 mm



30 L Drum, Disposal 25 L 30 L 3.4 kg 560 mm 280 mm 0.5 mm

18 L Returnable Drum 18 L 20 L 6.6 kg 442 mm 278 mm 1.5 mm

Some packaging options may not be available in your region. Please contact your sales representative to inquire.

Worldwide Packaging Options

Standard drums and characteristics

Description Capacity Total Capacity Weight Height Diameter Wall thickness

20 L Returnable Drum 20 L 22 L 8 kg 20 inches 11 inches 1.5 mm

50 L Returnable Drum 50 L 55 L 15 kg 23 inches 16 inches 1.5 mm

200 L Returnable Drum 200 L 220 L 47 kg 38 inches 24 inches 2 mm

200 L Returnable Drum, Level Sensor 200 L 220 L 47 kg 38 inches 24 inches 2 mm

Other containers available upon custom packaging request, please inquire your sales representative.

Additional Packaging Options (U.S. Only)


7

Products

Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Pharmadite® for Pharmaceutical Applications . . . . . . . . . . . . . . . . . . . . . . . . . 8

DNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Fast Deprotection Chemistries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

2'O-Methyl RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

DMT-2'Fluoro Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Labels and Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Non-Standard Nucleosides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Phosphate-ON Phosphoramidite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

NPPOC Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Solid Supports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Controlled Pore Glass and Columns — CPG Free Flow . . . . . . . . . . . . . . . . 42

Columns for Synthesizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Amino-ON CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Universal CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Liquid Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Activator 42® . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Product List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

QCStarting Matl.

SpecificationsIn-Process

ControlsIn-Process

Controls

QCBulk

Specifications

QCPackaged MatlSpecifications

Synthesis HPLCPurification

Drying Packaging

DMT-dNucleoside

CrudePhosphoramidite

PurifiedPhosphoramidite

BulkPhosphoramidite

PackagedPhosphoramidite

*EMEA: European Medicines Agency, http://www.emea.eu.int

Features Benefits

• Consistent quality • Reproducibleoligonucleotidesynthesis

• Suitability as starting materialfor API manufacture

- Raw material control andtraceability

- Process control

- Validated analytical methods

- Tight specifications

- Known impurity profiles

• Accordance withregulatoryguidelines

• Very high purity • High productionefficiency

• Non-animal origin of startingmaterials

• TSE safety

• Available in large scale • Secure supply

• Supply through our worldwidesupply chain

• Long-term reliability

Products

Manufacturing

Pharmadite amidites are prepared from DMT-protected nucleosides and the phosphitylatingagent “bis-amidite.”

The crude phosphoramidites are then purified bypreparative HPLC, dried and packaged. To ensurethe highest quality, our production process beginswith starting materials that possess stringentspecifications and defined impurity profiles. OurHPLC production line is cleaned using validatedcleaning methods and cleaning verification isperformed prior to each batch. Reactions areconducted at a minimum synthesis scale of 50 kgper batch.

Each processing step is monitored using analyticalin-process controls, including HPLC.

Pharmadite for PharmaceuticalApplications

The Pharmadite product line represents a new

class of standard protected DNA and RNA

phosphoramidites designed with highly

controlled impurity profiles and exceptional

overall purity.

Pharmadite products fulfill all the requirements ofstarting materials for the manufacture of activepharmaceutical ingredients as defined in the EMEA“Note for guidance on chemistry of the new activesubstance,”* making them suitable building blocksfor oligonucleotide drugs.

Pharmadite amidites are manufactured in scales ofup to multi-hundred kilos, under certified ISO 9001quality systems at SAFC Supply Solutionsmanufacturing facility in Hamburg, Germany.

We start with traceable, non-animal and very pureraw materials, use highly controlled synthesis andpurification processes, validated analyticalmethods and cleaning processes, all governedwith strict change control and documentation toyield unprecedented high quality products withpurity ratings at 99.5% or higher for DNA and99.0% or higher for RNA.

All remaining impurities, if present, are identifiedand characterized at a level of 0.1%.

The high level of control and documentationimposed at every step of the production processsupport regulatory requirements to make Pharmaditeamidites ideal for pharmaceutical applications.

8

Pharmadite® for Pharmaceutical Applications

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/rna-pharmadite.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

RNA PharmaditesCharacteristic

Acceptance Limit

Appearance white to off-white powder or

granules

Appearance of Solution ≤10 Hazen (c = 0.2 M in ACN)

Solubility clear solution (c = 0.2 M in ACN)

HPLC Identification conforms

HPLC Purity ≥99.0% area

Specified Impurities See impurities table

Single Unspecified Impurity ≤0.1% area

31P NMR Purity ≥99.0% area

31P NMR P(III) Impurities

(@ 100 to 169 ppm)

≤0.3% area

31P NMR P(V) Impurities

(@ -25 to 99 ppm)

≤1.0% area

31P NMR ≥170 ppm Impurities

(@ 170 to 225 ppm)

not detected

Residual Solvent Content ≤3.0% (w/w)

Water Content ≤0.40% (w/w)

Origin of Nucleoside non-animal origin

Specified Impurities of DNA Pharmadites A C G T

DMT-dNucleoside-cyanoethyl-H-phosphonate ≤0.3% ≤0.3% ≤0.3% ≤0.3%

DMT-dNucleoside phosphoramidate ≤0.3% ≤0.3% ≤0.3% ≤0.3%

DMT-dNucleoside-diisopropylamino-H-phosphonate not specified not specified ≤0.3% not specified

03'-Benzoyl-O5'-DMT-dC(bz) not applicable ≤0.3% not applicable not applicable

Specified Impurities of RNA Pharmadites A C G U

2'O-Amidite-3'O-TBDMS-5'O-DMT-rNucleoside ≤0.3% area ≤0.3% area ≤0.3% area ≤0.3% area

DMT-rNucleoside TBDMS ≤1.0% area ≤1.0% area ≤1.0% area ≤1.0% area

DMT-rNucleoside TBDMS-cyanoethyl-H-phosphonate ≤1.0% area ≤1.0% area ≤1.0% area ≤1.0% area

DMT-rNucleoside TBDMS-phosphoramidate ≤1.0% area ≤1.0% area ≤1.0% area ≤1.0% area

Specifications

Pharmadite amidites are characterized by theirexceptional purity and well-defined impurity profile.In particular, they are essentially free fromcontaminants which interfere in coupling reactions,such as other nucleosidic or non-nucleosidicphosphoramidites (P(III)-contaminants).

All remaining impurities in Pharmadite amidites, ifpresent, are identified, characterized and quantified.The impact of any such defined impurities on thesynthesis of oligonucleotides is well understood andhas been shown to be insignificant.

9

DNA PharmaditesCharacteristic

Acceptance Limit

Appearance white to off-white powder or

granules

Appearance of Solution ≤10 Hazen (c = 0.2 M in ACN)

Solubility clear solution (c = 0.2 M in ACN)

Identification conforms

HPLC Purity ≥99.5% area

Specified impurities ≤0.3% area, see impurities table

Single Unspecified Impurity ≤0.1% area

31P NMR Purity ≥99.5% area

31P NMR P(III) Impurities

(@ 100 to 169 ppm)

≤0.1% area

31P NMR P(V) Impurities

(@ -25 to 99 ppm)

≤0.5% area

31P NMR ≥170 ppm Impurities

(@ 170 to 225 ppm)

not detected: S/N < 2.5

Residual Solvent Content ≤3.0% wt

Water Content ≤0.40% wt

Origin of Nucleoside non-animal origin

Pharmadite® for Pharmaceutical Applications

10

Quality system and production process designed to meetpharmaceutical standards.

Control of starting materials and production processis a key factor in the synthesis procedure of RNAPharmadite. The phosphitylating reagent is controlledat a level of 0.1% P(III)- impurities. RNA Pharmaditeamidites are purified by preparative HPLC in a highlyautomated purification plant. ISO 9001 certified since1993, we guarantee reproducible quality withpredictable and controlled production:

• Robust process parameters

• In-process controls with specifications

• Batch integrity

• Change control

• Batch record review

• Process database and trend analysis

• Validated cleaning procedures

Products

DNA PharmaditesCatalog No. Description

A111P00-C DMT-dA(bz) Pharmadite

C111P00-C DMT-dC(bz) Pharmadite

G111P00-C DMT-dG(ib) Pharmadite

T111P00-C DMT-dT Pharmadite

RNA Pharmadites A211P00-C DMT-2'O-TBDMS-rA(bz) Pharmadite

C213P00-C DMT-2'O-TBDMS-rC(ac) Pharmadite

G211P00-C DMT-2'O-TBDMS-rG(ib) Pharmadite

U211P00-C DMT-2'O-TBDMS-rU Pharmadite

dA(bz) Phosphoramidite

dC(bz) Phosphoramidite

dG(ib) Phosphoramidite

dT Phosphoramidite

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/rna-pharmadite.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

11

DNA Phosphoramidites

SAFC Supply Solutions’ world-class expertise in

nucleic acid synthesis began in 1983 when Dr.

Hubert Köster first commercialized the synthesis

of ß-cyanoethylphosphoramidites. Since then,

the company has refined and per fected the

production of DNA and RNA phos phoramidites.

Today, SAFC Supply Solutions offers the highest

quality phosphoramidites in the industry.


Key Features of DNA Phosphoramidites

• Exocyclic amine functions are protected by abenzoyl group (dA(bz) and dC(bz)) orisobutyryl group (dG(ib))

• Recommended cleavage and deprotectionconditions are 8 hours at 55°C or 24 hours atroom temperature using concentrated ammoniasolution, for standard base-protectedoligonucleotides

• The high coupling efficiency of ProligoReagents’ DNA phosphoramidites leads tohigh-yield, high-quality oligonucleotides


Standard DNA PhosphoramiditesCompatible with Expedite and Polygen Instruments

Catalog No. Description Unit

A111081-12 DMT-dA(bz) Amidite 12 x 1 g

C111081-12 DMT-dC(bz) Amidite 12 x 1 g

G111081-12 DMT-dG(ib) Amidite 12 x 1 g

T111081-12 DMT-dT Amidite 12 x 1 g





Compatible with ABI Instruments













Standard DNA Phosphoramidites (cont.)Compatible with MerMade Instruments (8oz 28/400 bottle)









Compatible with Äkta and Oligo Pilot Instruments (100 ml septum bottle)













Bulk Quantities (16 oz 28/400 bottle)









Customized packaging

Bulk packaging up to multiple kg per containerand customized packaging with alternativequantities of amidites are available upon request.

Fast Deprotection Chemistries

The deprotection step of automated

oligonucleotide synthesis is integral to synthesis

time and final product quality. We offer various

fast deprotection chemistries for the rapid and

high-yield synthesis of high-purity.

1. Substitution of dC(bz) with dC(ac) —Beckman licenced method

Proligo® Reagents’ portfolio of oligonucleotidesynthesis reagents with acetyl-protectedphosphoramidtes and CPG has a license forBeckman Coulters’s fast deprotection chemistry.

Key Features of Acetyl-protectedphosphoramidtes

• Ultrafast deprotection (10 minutes at 65°C)

• Key component in oligonucleotide synthesis

• Industry standard for fast deprotection chemistry

• Operating for AMA methods without changes

• Consistent lot-to-lot high purity and performance

• Manufactured under a certified ISO 9001 quality system

12

Products Fast Deprotection Chemistries

* ≥25% ammonia in water

** Mixture of ≥25% ammonia in water with 40% aqueousmethylamine I/I, v/v

Overview

Fast deprotectionmethods

Monomers Cleavage anddeprotectionreagents

Time/Temperature

Substitution ofdC(bz) with dC(ac)(Beckmannmethod)

dA(bz),dC(ac),dG(ib), dT

AMA reagent** 10 min. at 65°C

TAC chemistry

dA(tac),dC(tac),dG(tac), dT

Concentratedammonia*

15 min. at 55°Cor 2 hrs. at room temp.

AMA reagent**5 min. at 65°C or 30 min. at room temp.

dG(dmf) methoddA(bz),dC(bz),dG(dmf), dT

Concentratedammonia*

2 hrs at 55°Cor 1 hr. at 65°C

Substitution ofdC(bz) with dC(tac)

dA(bz),dC(tac),dG(ib), dT

AMA reagent** 10 min. at 65°C

dC(ac) Phosphoramidite

OO

N

N

HN

O

OP

NO

CN

MeO

OMe

O

dC(tac) Phosphoramidite dG(dmf) Phosphoramidite

2. TAC Chemistry

Substitution of standard protecting groups with thelabile TAC (tert.butylphenoxyacetyl) protectinggroup results in ultra-fast and easy deprotectionunder mild conditions, suitable for oligonucleotideswith base-labile monomers and reporters as wellas in-situ synthesis schemes on glass surfaces.

13

4. Substituting the dC Protecting Group

Changing the dC protecting group to the TACprotecting group leads to rapid synthesis of high-purity and high-yield oligonucleotides. Substitutingthe commonly employed dC(bz) monomer by thedC(tac) monomer enables the application of ultra-fast deprotection with the AMA reagent andprovides a high-throughput method ofoligonucleotide synthesis.

Key Features of Substituting the dCProtecting Group

• The deprotection of oligonucleotide synthesisproducts with the AMA reagent is ultra-fast:complete deprotection requires 10 minutes at 65°C

• Side reactions at C-monomers throughtransamination are eliminated

• Not compatible with some base-labile modifiednucleosides

• dC(tac)-amidite can directly substitute for dC(bz)-amidite

• No change is required in the reagentscommonly used for DNA synthesis: acetonitrileis used to dissolve the amidite. The standardacetic anhydride capping reagent can beemployed

Key features of TAC Chemistry

• Deprotection of the TAC group is ultra-fast:complete deprotection in concentratedammonia occurs within 15 minutes at 55°C ortwo hours at room temperature

• Compatible with the AMA deprotection reagent(a mixture of ≥25% ammonia in water with 40%aqueous methylamine I/I, v/v)

• Highly soluble in acetonitrile. No need to addco-solvents such as dimethylformamide ormethylene chloride

• Suitable for the synthesis of oligomers withbase-labile units e.g., dyes and modifiers,because of less exposure to ammonia and thepossibility of room temperature deprotection

• No change is required in the reagentscommonly used for DNA synthesis, except thatProligo Reagents’ Fast Deprotection Cap Asolution is used instead of Cap A solution

• The application of dA(tac) minimizesdepurination and improves the quality ofoligonucleotides

3. dG(dmf) Method

Changing the dG protecting group to thedimethylformamidine (dmf) base-protecting groupenables rapid synthesis of high-purity, high-yieldoligonucleotide, thus increasing the efficiency ofhigh-throughput production.

Key Features of dG(dmf)

• dG(dmf) is deprotected faster than theconventional dG(ib): the deprotection time inconcentrated ammonia is reduced to 2 hours at55°C or 1 hour at 65°C

• The dG(dmf)-monomer is especially suitable forG-rich sequences: incomplete deprotection isgreatly reduced in comparison with theconventional dG(ib)-monomer

• dG(dmf)-amidite is as stable in solution as thestandard dA(bz)-, dC(bz)- and dT-amidites

• dG(dmf)-amidite can directly substitute fordG(ib)-amidite

• No change is required in the reagentscommonly used for DNA synthesis (except alow concentration iodine oxidizer i.e., 0.02 M iniodine, should be employed)

Fast Deprotection PhosphoramiditesCompatible with Expedite and Polygen Instruments


C113081-12 DMT-dC(ac) Amidite 12 x 1 g


A112081-12 DMT-dA(tac) Amidite 12 x 1 g

C112081-12 DMT-dC(tac) Amidite 12 x 1 g

G112081-12 DMT-dG(tac) Amidite 12 x 1 g




G115081-12 DMT-dG(dmf) Amidite 12 x 1 g
















Compatible with MerMade Instruments (8oz 28/400 bottle)
















Products

14

Fast Deprotection Chemistries

15

RNA Phosphoramidites, 2'O-Methyl RNA Phosphoramidites

RNA Phosphoramidites

RNA plays a pivotal role in biological systems due to its numerous functions in the transfer andprocessing of genetic information. The uniqueproperties of RNA have stimulated thedevelopment of a variety of applications indiagnostics and therapeutics, as well as in basicmolecular biology research where RNA can beused as:

• Catalytic agents (ribozymes)

• Affinity ligands (aptamers)

• Agents to induce gene silencing (RNA interference)

RNA interference (RNAi) has become a populartool for the sequence-specific inhibition of geneexpression and can be used in target validationand other drug development techniques. The mostconvenient method to provide sequence-specificRNA oligonucleotides is chemical synthesis on asolid support with RNA phosphoramidites and RNACPG, analogous to DNA synthesis.

RNA Phosphoramidites, 2'O-Methyl RNAPhosphoramidites

Modern phosphoramidite mediated synthesis

has enabled routine high yielding preparations of

RNA- and 2'O-Methyl RNA oligonucleotides. High

quality RNA amidites are key to low failure rates,

high biological activity of synthesis products and

cost effectiveness. SAFC Supply Solutions

provides high purity RNA amidites and 2'O-

Methyl RNA amidites. RNA monomers carry the

industry standard 2'-TBDMS protective group.

Standard RNA Amidites

• Industry standard 2'-TBDMS protective group

• Consistent lot-to-lot purity and performance

• Compatible with deprotection methods basedon methylamine or AMA

• Standard RNA amidites provide excellentcoupling results when used with ETT or BTT asactivator; best results are obtained withActivator 42

• Capping with standard acetic anhydridecapping reagent rather than with FastDeprotection Cap A

• Manufactured under a certified ISO 9001quality system

RNA Phosphoramidites with FastDeprotection Chemistry

Advantages of synthesis with TAC-protectedRNA phosphoramidites

• Increased synthesis yield and reducedpurification efforts

• Dramatically reduced deprotection times

• Minimized exposure to alkaline deprotection medium

• Minimized chain degradation during deprotection

http://www.sigmaaldrich.com/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/standard-rna-phosphoramidites.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

16

Products

N

N

N

OO

N

OP

NO

CN

MeO

OMe

OTBDMS

HN

O

DMT-rA(bz) PhosphoramiditeChemical Formula: C53H66N7O8PSi

Formula Weight: 988.2

Storage: ≤ -10°C

DMT-rAdenosine(N6-bz)(2'O-TBDMS)-ß-Cyanoethylphosphoramidite

DMT-rC(ac) PhosphoramiditeChemical Formula: C47H64N5O9PSi


Storage: ≤-10°C

DMT-rCytidine(N4-ac)(2'OTBDMS)-ß-Cyanoethylphosphoramidite

OO

N

N

HN

O

OP

NO

CN

MeO

OMe

O

OTBDMS

DMT-rG(ib) PhosphoramiditeChemical Formula: C50H68N7O9PSi


Storage: ≤-10°C

DMT-rGuanosine(N2-ib)(2'O-TBDMS)-ß-Cyanoethylphosphoramidite

DMT-rU PhosphoramiditeChemical Formula: C45H61N4O9PSi


Storage: ≤-10°C

DMT-rUridine(2'O-TBDMS)-ß-Cyanoethylphosphoramidite

N

N

NH

O

OO

N

OP

NO

CN

MeO

OMe

NH

OTBDMS

O

OO

N

HN

O

O

OP

NO

CN

MeO

OMe

OTBDMS

deprotection of the RNA oligomer, e.g., with a solutionof tetrabutylammonium fluoride (TBAF) in tetra -hydrofane (THF) or with triethylamine hydrofluoride.

RNA Synthesis

The synthesis cycle for RNA oligonucleotidesconsists of the same series of reactions as thecycle that is employed for DNA monomers.

However, the rate of coupling for RNA monomersis slower, compared to that of DNA monomers (forRNA monomers a coupling time of 10 minutes or 6minutes using Activator 42 is recommendedcompared to 90 seconds for DNA monomers).With the exception of the monomers and supports,RNA synthesis is accomplished with the samereagents as DNA synthesis.

All RNA phosphoramidites are diluted with dry acetonitrile.

User Instructions

RNA monomers feature hydroxyl groups at the 2'-position. In order to prevent the formation of unnatural2'-5' phosphodiester bonds during chain elongation,the 2'OH group is protected with a trialkyl-silyl group,tert-butyldimethylsilyl (TBDMS). The TBDMS group isstable under the acidic conditions used to remove theDMT group during the synthesis cycle, but can beremoved by a variety of methods after cleavage and


RNA Phosphoramidites Compatible with Expedite and Polygen Instruments


A211081-01 DMT-2'O-TBDMS-rA(bz) Amidite 1 x 0.5 g

C213081-01 DMT-2'O-TBDMS-rC(ac) Amidite 1 x 0.5 g

G211081-01 DMT-2'O-TBDMS-rG(ib) Amidite 1 x 0.5 g

U211081-01 DMT-2'O-TBDMS-rU Amidite 1 x 0.5 g






A211061-01 DMT-2'O-TBDMS-rA(bz) Amidite 1 x 1 g

C213061-01 DMT-2'O-TBDMS-rC(ac) Amidite 1 x 1 g

G211061-01 DMT-2'O-TBDMS-rG(ib) Amidite 1 x 1 g

U211061-01 DMT-2'O-TBDMS-rU Amidite 1 x 1 g

Other quantities and packaging are available upon request.


17

DEPC (diethyl pyrocarbonate, stir 1L of HPLCgrade water with 100 �l DEPC overnight andautoclave twice) and use baked glassware(250°C+ for more than 4 hours).

9. Transfer the supernatant solution of the RNAoligonucleotide into a separate vial. The yieldof the RNA oligonucleotide can be improvedby rinsing the support with ethanol/ acetonitrile/water 3/1/1, v/v, and combining theoligonucleotide solution with the washingsolution. Evaporate to dryness.

10. Add a 1 M solution of tetrabutylammoniumfluoride (TBAF) in THF and incubate for 24hours at room temperature. The deprotectiontime can be shortened to 6 hours if a TBAF-solution, with water content less than 5%, w/w,is employed. Following deprotection, add anequal volume of 1 M TEAA buffer pH 7,followed by another volume of water.Alternatively, deprotection can beaccomplished using a mixture of neattriethylamine trihydrofluoride, triethylamineand N-methylpyrrolidon, 4/3/6, v/v, which canbe employed for 90 minutes at 65°C. Thedeprotection reaction is quenched by theaddition of an equal volume of water in thiscase. Note that the application of triethylaminetrihydrofluoride in the DMT-On mode will leadto detritylation, due to the acidity of thereagent.

11. Desalt the RNA oligonucleotide by using adesalting matrix such as Sephadex® G25, anion exchange cartridge, or a reversed phasepurification cartridge. Optimal conditions fordesalting vary greatly with the employedmatrix/product. Conditions recommended bythe manufacturer should generally be applied.The lyophilized crude RNA oligonucleotideproduct can be purified by AX-HPLC or bypreparative gel electrophoresis.

User Instructions (continued)

1. Use anhydrous acetonitrile (water content≤30 ppm) as diluent. It is important tomaintain anhydrous conditions whiledissolving RNA amidites in acetonitrile.

2. For use on PE 8900 instruments, add 10 mlof acetonitrile to 0.5 g RNA monomer, toobtain a concentration of 50 mg/ml. For useon PE 390 series instruments, add 5 mlacetonitrile to 0.5 g RNA monomer to obtaina concentration of 100 mg/ml.

3. Gently swirl the vial until the powder iscompletely dissolved.

4. Attach the dissolved phosphoramidite to theappropriate position on the synthesizer.Ensure that the delivery line to the synthesischamber is sufficiently primed.

5. Enter the sequence of the RNAoligonucleotide you wish to synthesize. Aminimum coupling time of 10 minutes or 6minutes using Activator 42 is recommendedfor 2'-TBDMS protected RNA amidites.

6. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending onyour intended further use of the oligomer, youcan choose either DMT-On or DMT-Offprocedures. The coupling efficiency of RNAmonomers may be determined by standarddimethoxytrityl cation assays.

7. Cleave from the support and deprotect theRNA oligonucleotide with a mixture ofconcentrated ammonia and ethanol 3/1, v/v,at 55°C for 8 hours, or at room temperaturefor 24 hours. Alternatively, AMA reagent(concentrated ammonia/40% aqueousmethylamine 1/1, v/v) can be employed for10 minutes at 65°C.

8. It is essential to employ sterile conditionsfrom this step forward. Always use sterilizedwater: preferably water recently treated with

18

Products

Key Features of TAC-Protected RNAPhosphoramidites

• Base protected by a tert-butylphenoxyacetyl(TAC) group, in the same manner as DNAphosphoramidites

• Uses the same synthesizer protocols as recommended for bz/ib protected RNA monomers

• Follows the established DNA synthesis cycle,but with prolonged coupling times due to steric hindrance

• Same liquid reagents are used throughout thesynthesis cycle as in DNA synthesis, exceptthat Fast Deprotection Cap A reagent must beemployed with Proligo Reagent’s TAC-protected phosphoramidites

• Fast Deprotection Cap A contains tert-butylphenoxyacetyl acetic anhydride (tac2O) intetrahydrofuran, which ensures that thedisplacement of tert-butylphenoxyacetyl (TAC)on guanine bases does not occur

• Cleavage and deprotection procedures arecomparable with those of DNA synthesis, withan additional step to remove the 2'OH protecting group

• 2'OH function is protected by a tert-butyldimethylsilyl (TBDMS) group to preventderivatization and degradation during thesynthesis cycle

Although our TAC-protected RNA monomersdisplay sufficient stability in solution over several days, we recommend to reconstitute freshamidites after 6 days on the instrument to achieveoptimal results.


N

N

N

N

OO

O

HNOCH3

CH3O

O

OTBDMS

PN(iPr)2O

CN

O

rA(tac) PhosphoramiditeChemical Formula: C58H76N7O9PSi


Storage: ≤-10°C

DMT-rAdenosine (N6-tac)(O2'-TBDMS)-ß-Cyanoethylphosphoramidite

rC(tac) PhosphoramiditeChemical Formula: C57H76N5O10PSi


Storage: ≤-10°C

DMT-rCytidine(N4-tac)(O2'-TBDMS)-ß-Cyanoethylphoshoramidite

N

OO

O

OCH3

CH3O

N

O

HN

O

PO

CN(iPr)2

N

OTBDMS

O

rG(tac) PhosphoramiditeChemical Formula: C58H76N7O10PSi


Storage: ≤-10°C

DMT-rGuanosine(N2-tac)(O2'-TBDMS)-ß-Cyanoethylphosphoramidite

rU PhosphoramiditeChemical Formula: C45H61N4O9PSi


Storage: ≤+10°C

DMT-rUridine(O2'-TBDMS)-ß-Cyanoethylphosphoraamidite

N

NH

N

N

OO

O

OCH3

CH3O

PO

CNN(iPr)2

O

NH

O

O

OTBDMS

N

OO

O

OCH3

CH3O

HN

O

PO

CN(iPr)2

N

O

OTBDMS


19

Fast Deprotection RNA PhosphoramiditesCompatible with Expedite and Polygen Instruments


A212081-01 DMT-2'O-TBDMS-rA(tac) Amidite 1 x 0.5 g

C212081-01 DMT-2'O-TBDMS-rC (tac) Amidite 1 x 0.5 g

G212081-01 DMT-2'O-TBDMS-rG(tac) Amidite 1 x 0.5 g







A212061-01 DMT-2'O-TBDMS-rA(tac) Amidite 1 x 1 g

C212061-01 DMT-2'O-TBDMS-rC (tac) Amidite 1 x 1 g

G212061-01 DMT-2'O-TBDMS-rG(tac) Amidite 1 x 1 g


Compatible with MerMade Instruments





Bulk Quantities






Bulk packaging up to multiple kg per container andcustomized packaging with alternative quantities ofamidites are available upon request.

20

Products

RNA Supports

The supports for RNA synthesis consist of an RNAnucleoside covalently attached through either the2'- or the 3'-position to controlled pore glass (CPG).The remaining free hydroxyl group is protected witha base-labile acyl group. The pore size of ProligoReagents’ CPG for RNA synthesis is 500Å. ProligoReagents offers ready-to-use synthesis columns forRNA synthesis at 1 �mol scale.

RNA Synthesis

The synthesis cycle for RNA oligonucleotidesconsists of the same series of reactions as thecycle that is employed for Fast Deprotection DNAmonomers. However, the rate of coupling for RNAmonomers is slower, compared to that of DNAmonomers (a coupling time of 10 minutes for RNAmonomers is recommended compared to 90seconds for DNA monomers). With the exceptionof the monomers and supports, RNA synthesis isaccomplished with the same reagents as DNAsynthesis.

All RNA phosphoramidites from Proligo Reagentsare diluted with dry acetonitrile. Fast DeprotectionCap A is employed to prevent the transacylation ofguanosine bases, similar to synthesis of tert-butylphenoxyacetyl (TAC) DNA monomers.

RNA Monomers

RNA monomers feature hydroxyl groups at the 2'-position. In order to prevent the formation ofunnatural 2'-5' phosphodiester bonds during chainelongation, the 2'OH group is protected with atrialkyl-silyl group, tert-butyldimethylsilyl (TBDMS).The TBDMS group is stable under the acidicconditions used to remove the DMT group duringthe synthesis cycle, but can be removed by avariety of methods after cleavage and deprotectionof the RNA oligomer, e.g., with a solution oftetrabutylammonium fluoride (TBAF) intetrahydrofan (THF) or with triethylaminehydrofluoride.

TAC RNA Monomers

RNA oligonucleotides prepared from TAC protectedRNA monomers can be base-deprotected undervery mild conditions. Recommended cleavage anddeprotection conditions for TAC base-protectedoligonucleotides are 15 minutes at 55°C or 2 hoursat room temperature, in a mixture of concentratedammonia solution and ethanol (3/1, v/v).Alternatively, AMA reagent (concentratedammonia/40% aqueous methylamine 1/1, v/v) canbe employed for 30 minutes at room temperature.The shorter exposure time of the oligonucleotide tothe alkaline deprotecting agent, compared toconventionally protected RNA oligonucleotides,reduces chain degradation and provides a higheryield of full length RNA product.

Although Proligo Reagents’ TAC RNA monomersare stable for several days in solution, werecommend reconstitution of fresh amidites after 6days on the instrument, to achieve optimal results.

ODMTO

O OTBDMS

Base OHO

O OTBDMS

Base

OO

O

DMT

PO

CNN(iPr)

2

Base

OTBDMS

OO

O

DMT

PO

CN

OO

O

Base

Base

OTBDMS

OTBDMS

OO

O

Base

OTBDMS

O

O

OO

O

DMT

PO O

OO

O

CN

Base

Base

OTBDMS

OTBDMS

Final: Cleavage/Deprotection

1. Deblocking

4. Oxidation

3. Capping

Start next cycle:1. Deblocking

2. Activation and Coupling

Solid SupportSolid Support

Solid Support

Solid Support

Solid Support

Fast Deprotection RNA Synthesis Cycle



21

10. It is essential to employ sterile conditions fromthis step forward. Always use sterilized water:preferably water recently treated with DEPC(diethyl pyrocarbonate, stir 1 L of HPLC gradewater with 100 ml DEPC overnight andautoclave twice) and use baked glassware(250°C+ for more than 4 hours).

11. Transfer the supernatant solution of the RNAoligonucleotide into a separate vial. The yieldof the RNA oligonucleotide can be improvedby rinsing the support with ethanol/ acetonitrile/water 3/1/1, v/v, and combining theoligonucleotide solution with the washingsolution. Evaporate to dryness.

12. Add a 1M solution of tetrabutylammoniumfluoride (TBAF) in THF and incubate for 24 hours at room temperature. Thedeprotection time can be shortened to 6 hours if a TBAF-solution, with water contentless than 5%, w/w, is employed. Followingdeprotection, add an equal volume of 1 MTEAA buffer pH 7, followed by anothervolume of water. Alternatively, deprotectioncan be accomplished using a mixture of neattriethylamine trihydrofluoride, triethylamineand N-methylpyrrolidon, 4/3/6, v/v, which canbe employed for 90 minutes at 65°C. Thedeprotection reaction is quenched by theaddition of an equal volume of water in thiscase. Note that the application of triethyl -amine trihydrofluoride in the DMT-On modewill lead to detritylation, due to the acidity ofthe reagent.

13. Desalt the RNA oligonucleotide by using adesalting matrix such as Sephadex® G25, anion exchange cartridge, or a reversed phasepurification cartridge. Optimal conditions fordesalting vary greatly with the employedmatrix/product. Conditions recommended bythe manufacturer should generally be applied.The lyophilized crude RNA oligonucleotideproduct can be purified by AX-HPLC or bypreparative gel electrophoresis.

User Instructions

1. Use anhydrous acetonitrile (water content ≤30ppm) as diluent. It is important to maintainanhydrous conditions while dissolving RNAamidites in acetonitrile.

2. For use on Expedite instruments, add 10 mlof acetonitrile to 0.5 g RNA monomer, toobtain a concentration of 50 mg/ml. For useon ABI instruments, add 5 ml acetonitrile to0.5 g RNA monomer to obtain a concentrationof 100 mg/ml.



5. Once TAC RNA phosphoramidite has beendissolved and placed on your instrument, thephosphoramidite should be used within 6 days.

6. Enter the sequence of the RNAoligonucleotide you wish to synthesize. Aminimum coupling time of 10 minutes or 6minutes using Activator 42 is recommendedfor 2'-TBDMS-protected RNA amidites.

7. Fast deprotection Cap A must be employed inall RNA synthesis with the TAC-protected rGRNA phosphoramidite.

8. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending on yourintended further use of the oligomer, you canchoose either DMT-On or DMT-Offprocedures. The coupling efficiency of RNAmonomers may be determined by standarddimethoxytrityl cation assays.

9. Cleave from the support and deprotect the RNA oligonucleotide with a mixture of concentrated ammonia and ethanol 3/1,v/v, at 55°C for 15 minutes, or at roomtemperature for 120 minutes. Alternatively,AMA reagent (concentrated ammonia/40%aqueous methylamine 1/1, v/v) can beemployed for 10 minutes at 65°C.

22

Products RNA Phosphoramidites, 2'O-Methyl RNA Phosphoramidites

2'O-Methyl RNA Phosphoramidites

2'O-Methyl RNA is a nucleic acid analog that is

characterized by the exceptional hybridization

properties that it imparts with complimentary

DNA or RNA, as well as increased stability

against enzymatic degradation compared to

natural nucleic acids.

The unique combination of properties of 2'O-Methyl RNA had found widespread use in the fields of:

• Diagnostic probes

• Aptamer and ribozyme development

• Mixed 2'O-Methyl-RNA/DNA antisensemolecules

2'O-Methyl RNA nucleoside can be advantageouslyincorporated in nucleic acid probes with RNA orDNA for in-vivo or in-vitro applications to conveynuclease resistance.

Key features of 2'O-Methyl RNAPhosphoramidites

• High yield of crude oligonucleotides

• Compatible with DNA synthesis

• Can be employed together with DNA or RNAphosphoramidites in the same synthesis toproduce mixmer oligonucleotides

• Recommended deprotection conditions are 8 hours at 55°C using concentratedammonia solution, or with AMA (concentratedammonia/40% aqueous methylamine I/I, v/v) for10 minutes at 65°C

• Purification and other downstream processingof fully modified 2'O-Methyl RNAoligonucleotides are simpler than in the case ofRNA, as no special precautions are required toprovide protection against nucleolyticdegradation

• Synthesis of 2'O-Methyl RNA oligonucleotidesis similar to standard DNA synthesis, but requires an elongatedcoupling time (recommended is 6 minutescompared to 90 seconds for DNA monomers)

• 2'O-Methyl RNA phosphoramidites are alsoavailable with fast deprotection chemistrysolutions.

2’0-Methyl-rA(bz) PhosphoramiditeChemical Formula: C48H54N7O8P


Storage: ≤+10°C

DMT-2'O-Methyl-rAdenosine(N6-Benzoyl)-ß-Cyanoethylphosphoramidite

2’0-Methyl-rU PhosphoramiditeChemical Formula: C40H49N4O9P


Storage: ≤+10°C

DMT-2'O-Methyl-rUridine-ß-Cyanoethylphosphoramidite

N

N

N

N

OO

O

HNOCH3

CH3O

O

OCH3

PN(iPr)2O

CN

N

OO

O

OCH3

CH3O

HN

O

PO

CN(iPr)2

N

O

OCH3

2’O-Methyl-rC(ac) PhosphoramiditeChemical Formula: C42H52N5O9P


Storage: ≤-10°C

DMT-2'O-Methyl-rCytidine(N4-acetyl)-ß-Cyanoethylphosphoramidite

N

N

OO

O

HNOMe

MeOO

O

OMeP

CN

O

N


23

2’0-Methyl-rC(tac) PhosphoramiditeChemical Formula: C52H64N5O10P


Storage: ≤-10°C

DMT-2'O-Methyl-rCytidine(N4-tac)-ß-Cyanoethylphosphoramidite

N

OO

O

OCH3

CH3O

N

O

HN

O

PO

CN(iPr)2

N

OCH3

O

2’0-Methyl RNA PhosphoramiditesCatalog No. Description Unit

Compatible with Expedite Instruments

A211181-01 DMT-2'O-Me-rA(bz) Amidite 1 x 0.5 g

A212181-01 DMT-2'O-Me-rA(tac) Amidite 1 x 0.5 g

C212181-01 DMT-2'O-Me-rC(tac) Amidite 1 x 0.5 g

C213181-01 DMT-2'O-Me-rC(ac) Amidite 1 x 0.5 g

G211181-01 DMT-2'O-Me-rG(ib) Amidite 1 x 0.5 g

G212181-01 DMT-2'O-Me-rG(tac) Amidite 1 x 0.5 g

U211181-01 DMT-2'O-Me-rU Amidite 1 x 0.5 g









A211161-01 DMT-2'O-Me-rA(bz) Amidite 1 x 1 g

C212161-01 DMT-2'O-Me-rC(tac) Amidite 1 x 1 g

C213161-01 DMT-2'O-Me-rC(ac) Amidite 1 x 1 g

G211161-01 DMT-2'O-Me-rG(ib) Amidite 1 x 1 g

U211161-01 DMT-2'O-Me-rU Amidite 1 x 1 g

Bulk Quantities


A212110-01 DMT-2'O-Me-rA(tac) Amidite 1 x 10 g



G212110-01 DMT-2'O-Me-rG(tac) Amidite 1 x 10 g



Bulk packaging up to multiple kg per container andcustomized packaging with alternative quantities ofamidites are available upon request.

2’0-Methyl-rG(ib) PhosphoramiditeChemical Formula: C45H56N7O9P


Storage: ≤+10°C

DMT-2'O-Methyl-Guanosine(N2-Isobutyryl)-ß-Cyanoethylphosphoramidite

N

NH

N

N

OO

O

OCH3

CH3O

PO

CNN(iPr)2

O

NH

O

OCH3

24

Products

Base Protection

Proligo Reagents’ 2'O-Methyl RNA monomers arecompatible with fast deprotection schemes that arebased on the application of aliphatic amines, suchas methylamine. The adenosine and guanosinemonomers are protected with the standard benzoyland isobutyryl groups. The uridine monomer isunprotected at the base, and the cytidine monomeris protected with a TAC (tert-butylphenoxyacetyl)group. This protecting group avoids transaminationside reactions at cytidines, when alkylamines areemployed in the deprotection reaction. AMAreagent (concentrated ammonia/40% aqueousmethylamine 1/1, v/v) can be conveniently applied.

2'O-Methyl RNA Supports

The supports for 2'O-Methyl oligoribonucleotidesynthesis consist of a 2'O-Methyl RNA nucleosidecovalently attached through the 3'-position tocontrolled pore glass (CPG). The pore size ofProligo Reagents’ CPG for 2'O-Methyl oligo ribo -nucleotide synthesis is 500Å. Proligo Reagentsoffers ready-to-use synthesis columns for 2'O-Methyloligoribonucleotide synthesis at 1 �mol scale.


2'O-Methyl RNA Synthesis

The synthesis cycle for 2'O-Methyl-oligoribonucleotides consists of the same series ofreactions as the cycle that is employed for DNAmonomers. However, the rate of coupling for 2'O-Methyl RNA monomers is slower compared to thatof DNA monomers (a coupling time of 6 minutes isrecommended for 2'O-Methyl RNA monomerscompared to 90 seconds for DNA monomers).

With the exception of the 2'O-Methyl RNA monomersand supports, RNA synthesis is accomplished withthe same reagents as DNA synthesis.

All 2'O-Methyl RNA phosphoramidites from ProligoReagents are diluted with dry acetonitrile.

2'O-Methyl RNA Monomers

2'O-Methyl RNA monomers feature methoxygroups at the 2'-position. The methoxy groups areperfectly stable in all conditions employed in theassembly of oligonucleotides by automatedphosphoramidite synthesis, and in all standardalkaline deprotection conditions.

ODMTO

O OCH3

Base OHO

O OCH3

Base

OO

O

DMT

PO

CNN(iPr)2

Base

OCH3

OO

O

DMT

PO

CN

OO

O

Base

Base

OCH 3

OCH3

OO

O

C

O

CH3 Base

OCH 3

OO

O

DMT

PO O

OO

O

CN

Base

Base

OCH 3

OCH 3

Final: Cleavage/Deprotection

1. Deblocking

4. Oxidation

Solid SupportSolid Support

Solid Support

Solid Support

Solid Support3. Capping

Start next cycle:1. Deblocking

2. Activation and Coupling

The Synthesis Cycle


25

Methods

1. Use anhydrous acetonitrile (water content ≤30ppm) as diluent. It is important to maintainanhydrous conditions while dissolving RNAphosphoramidites in acetonitrile.

2. For use on Expedite instruments, add 10 ml ofacetonitrile to 0.5 g 2'O-Methyl RNA monomer,to obtain a concentration of 50 mg/ml. For useon ABI instruments, add 5 ml acetonitrile to0.5 g 2'O-Methyl RNA monomer, to obtain aconcentration of 100 mg/ml.


4. Attach the dissolved phosphoramidite to the appropriate position on the synthesizer.Ensure that the delivery line to the synthesischamber is sufficiently primed.

5. Enter the sequence of the 2'O-Methyloligoribonucleotide you wish to synthesize. Aminimum coupling time of 6 minutes isrecommended for 2'O-Methyl RNAphosphoramidites.

6. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending on yourintended further use of the oligomer, you canchoose either DMT-On or DMT-Offprocedures. The coupling efficiency of 2'O-Methyl RNA monomers may be determinedby standard dimethoxytrityl cation assays.

7. Cleave from the support and deprotect the2'O-Methyl oligoribonucleotide withconcentrated ammonia at 55°C for 8 hours.Alternatively, AMA reagent (concentratedammonia/40% aqueous methylamine 1/1, v/v)can be employed for 10 minutes at 65°C.

8. The 2'O-Methyl oligoribonucleotide is nowready for further processing, such asdesalting or purification with RP-HPLC, AX-HPLC or gel-based methods. Purification offully-modified 2'O-Methyl RNAoligonucleotides is simpler than in case ofRNA, as no special precautions are requiredto prevent nucleolytic degradation

26

Products DMT-2'Fluoro Phosphoramidites

DMT-2'Fluoro Phosphoramidites

2’Fluoro Phosphoramidites are used to

synthesize oligonucleotides that are more

thermally stable and provide increased

nuclease resistance.

Features of 2'Fluoro Phosphoramidites:

• Can be employed together with DNA or RNAphosphoramidites

• Recommended deprotection conditions are 8hours at 55°C using concentrated ammoniasolution, or with AMA for 10 minutes at 65°C

• Synthesis of 2'Fluoro oligonucleotides is similar to standard DNA synthesis, but requires an elongated coupling time(recommended is 3 minutes compared to 90 seconds for DNA monomers)

• Consistent lot-to-lot high purity andperformance


Please ask for delivery dates of these specialty amidites.

DMT-2'Fluoro-dU AmiditeDMT-2'Fluoro-dC(ac) Amidite

OO

N

N

HN

O

OP

NO

CN

MeO

OMe

O

F

OO

N

HN

O

O

OP

NO

CN

MeO

OMe

F

DMT-2'Fluoro PhosphoramiditesCatalog No. Description Unit

C213281-01 DMT-2'Fluoro-dC(ac) Amidite, 89 1 x 0.25 g

C213231-01 DMT-2'Fluoro-dC(ac) Amidite, ABI 1 x 0.25 g

C213233-01 DMT-2'Fluoro-dC(ac) Amidite, ABI 1 x 1 g

U211281-01 DMT-2'Fluoro-dU Amidite, 89 1 x 0.25 g

U211231-01 DMT-2'Fluoro-dU Amidite, ABI 1 x 0.25 g

U211233-01 DMT-2'Fluoro-dU Amidite, ABI 1 x 1 g

Analytical SpecificationsTest 2'Fluoro-dC(ac) 2'Fluoro-dU

HPLC Purity ≥98.0% ≥98.0%

31P-NMR ≥99% ≥99%

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/new-proligo-reagents.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

27

Labels and Modifications

Phosphoramidite technology is ideally suited for

the modification of synthetic oligonu cleotides

with covalently attached reporter moieties,

linkers, spacers or haptens. SAFC Supply

Solutions provides popular reporters and linkers

ready to use for DNA/RNA synthesis machines

such as ß-cyanoethyl phosphoramidites.

Fluorescein Phosphoramidite

Fluorescein phosphoramidite is composed of aprotected fluorescein molecule linked to a ß-cyanoethylphosphoramidite. The fluoresceinderivative consists of two isomers derived from 5-and 6-carboxy fluorescein. As a result, two peakswill be seen on a RP-HPLC chromatogram of thesynthesis product.

Key Features of the FluoresceinPhosphoramidite

• Readily soluble in acetonitrile

• Couples to the 5'-end of the oligonucleotideusing standard synthesis protocols

• Protecting groups on the fluorescein moiety areremoved under standard conditions of cleavageand deprotection with concentrated ammonia

• A detritylation step is not required since thefluorescein phosphoramidite does not contain adimethoxytrityl(DMT-) group

• The labeled oligonucleotide is ready for use in most applications after the evaporation ofammonia. Standard procedures can be used ifadditional purification is required

• The fluorescein moiety provides a purificationhandle in RP-HPLC purification

Biotin Phosphoramidite

Biotin-labeled oligonucleotides have becomeextremely popular in DNA capture and detectionapplications, due to their very high-sensitivity andstrong, specific binding affinity with avidin andstreptavidin proteins. Biotin-based detectionmethods and are widely used by researchers.Biotin labeling is compatible with PCR and mosthybridization techniques.

Key Features of the Biotin Phosphoramidite

• Behaves like any standard amidite on the DNA synthesizer

• Readily soluble in acetonitrile

• Biotin compound has a dimethoxytrityl (DMT)group on the ring structure, which allowscoupling-yield determination and trityl-selectivepurification

• A long, water-compatible linker arm ensuresmaximum sensitivity

• Provides a coupling efficiency of at least 95%

Labels and Modifications

28

Products Labels and Modifications

Amino Linkers

Amino linkers can be employed to conjugatebiotin, fluorescein or other modifiers and reportergroups to the 5'end of oligonucleotides, or toattach oligonucleotides to surfaces. SAFC SupplySolutions offers 2 monomethoxytrityl-protectedamino linkers (MMT-linkers) and 2 trifluoroacetylprotected amino linkers (TFA linkers):

• Trifluoroacetyl (TFA)-protected pentyl (C5)amino linker

• Trifluoroacetyl (TFA)-protected hexyl (C6)amino linker

• Monomethoxytrityl (MMT)-protected amino linker

• ssH-linker: the next generation of MMT linker

Monomethoxytrityl (MMT)-protected aminolinker

The MMT-group can be cleaved on the synthesisinstrument with acidic deblock solution to enableon-support labeling protocols. Alternatively, theMMT-amino linker can be attached in the trityl-onmode of the instrument to provide purificationhandle similar to the DMT-group of the con -ventional oligonucleotides. The MMT-group is thenremoved with aqueous acid after purification witheither RP-HPLC or a purification cartridge.

Trifluoroacetyl (TFA)-protected amino linker

The base-labile TFA-group is easily removed withconcentrated ammonia during the cleavage anddeprotection step. Additional deprotection stepsare not necessary.

ssH-linker

ssH-linker comprises an internal carbamate group,which is attached to the MMT-protected aminogroup via a short spacer. The carbamate moletyfacilitates the cleavage of the MMT-group undermildly acidic conditions while increasing thestability of the MMT-group during the deprotectionof the oligonucleotide with ammonia. Thecarbamate group also enhances the reactivity ofthe amino group through a neighbor group effect,and thereby accelerates conjugations to amino-reactive modifiers and reporters.

The MMT-group of ssH-linker serves as anexcellent purification handle after theoligonucleotide synthesis in trityl-on mode, similarto the DMT-group of conventional oglionucleotides.The MMT-group is cleaved under very mildconditions in aqueous acetic acid (10% glacialacetic acid in water, 20 min. room temp.)Alternatively, the MMT-group can be cleaved on thesynthesis instrument with acidic deblock solutionto enable on-support labeling protocols.

Key features of amino linkers

• Completely soluble in acetonitrile

• Base-labile TFA- as well as acid-labile MMT-protecting groups on the amino linker

• Amino linker products are coupled withstandard synthesis protocols, identical to the coupling of DNA monomerphosphoramidites

• No change in auxiliary synthesis reagents is required

• The MMT-amino linker features a lipophilicgroup which aids in purification of the modifiedoligonucleotide after synthesis

• The acid-labile MMT-group permits the colorimetricdetermination of the coupling efficiency

• It is recommended to deprotect MMT-amino linker oligonucleotides in concentrated ammonia at a lowertemperature e.g., at 40°C for 24 hours

• The MMT-group can be removed from theoligonucleotide at room temperature

- in case of MMT-amino linker with 80%aqueous acetic acid in 3 hours

- in case of ssH-linker with 10% aqueous aceticacid in 20 minutes

• TFA-amino linker is completely deprotectedwith concentrated ammonia. Additionaldeprotection steps are not necessary

29

Key features of ssH-linker:

• Advantages over conventional amino linkers

- Deprotection of the amino-group underexceptionally mild conditions which avoiddepurination side reaction

- Deprotection with 10% aqueous acetic acid atambient temperature for 20 minutes

- Better labeling efficiency than C6-amino linkers

- Higher coupling efficiency than C6-amino linkers

- Better trityl-on purification efficiency

• General features

- Excellent coupling efficiency

- Used with standard deblock, activator,oxidizer and capping-solutions

Custom products

Phosphoramidites of non-catalog linkers, reporters ormodifiers are offered as custom synthesis products.

Labels and ModificationsCompatible with Expedite and Polygen Instruments


M010982-01 ssH-Linker 1 x 0.25 g

M010882-01 TFA Hexylaminolinker 1 x 0.25 g

M010181-01 Fluorescein Amidite 1 x 0.1 g

M010282-01 MMT-Hexylamine-Linker Amidite 1 x 0.25 g

M010381-01 Biotin Amidite 1 x 0.1 g


M010682-01 TFA Pentylaminolinker Amidite 1 x 0.25 g


M010932-01 ssH-Linker 1 x 0.25 g

M010832-01 TFA Hexylaminolinker Amidite 1 x 0.25 g






Fluorescein Phosphoramidite Biotin Phosphoramidite

TFA Hexyl Amino Linker ssH-Linker

MMT-Amino Linker TFA Pentyl Amino Linker

30


Method

1. Use anhydrous acetonitrile (water content ≤30ppm) to dissolve the fluoresceinphosphoramidite. It is important to maintainanhydrous conditions when dissolving thefluorescein phosphoramidite in acetonitrile.

2. For use on Expedite instruments, add 2 mlacetonitrile to 0.1 g fluorescein phospho -ramidite (M010181-01) to obtain a con -centration of 50 mg/ml. For use on ABIinstruments, add 1.2 ml acetonitrile to 0.1 gfluorescein phosphoramidite (M010131-01) toprepare a 0.1 M solution.


4. Once the fluorescein phosphoramidite hasbeen dissolved and placed on your instru -ment, it should be used within 4 days. If youdo not plan to use all of the material in 4 days,remove the vial, seal carefully and store at –20°C until needed.


6. Enter the sequence of the oligonucleotide you wish to synthesize with fluoresceinphosphoramidite at the 5'-end. A minimalcoupling time of 3 minutes is recommendedfor fluorescein phosphoramidite.

7. Proceed as you would with a standard DNAoligonucleotide synthesis. Note that fluoresceinphosphoramidite from Proligo Reagents doesnot contain a DMT group. Oligonucleotides donot need to be detritylated at the end of thesynthesis. Note that the fluorescein phospho -ramidite will terminate the synthesis and canonly be employed in the last coupling step onthe 5' terminus.

8. Cleave and deprotect the oligonucleotide withammonia at 55°C for 8 hours with standardprotected nucleobases, or, if TAC-protectedphosphoramidites are used, at 55°C for 15minutes. The fluorescein-moiety is stableunder these conditions.

9. The oligonucleotide is now ready for furtherprocessing, such as desalting or purificationwith RP-HPLC, AX-HPLC or gel-based methods.The fluorescein label allows the purified fractionto be easily detected during collection.

10. Oligonucleotides labeled with fluoresceinshould be stored in the dark.

Fluorescein PhosphoramiditeChemical Formula: C46H58N3O10P


Storage: ≤-10°C

Fluorescein-ß-Cyanoethylphosphoramidite

31

Method

1. Use anhydrous acetonitrile (water content ≤30ppm) to dissolve the biotin phospho ramidite.It is important to maintain anhydrousconditions when dissolving the biotinphosphoramidite in acetonitrile.

2. For use on Expedite instruments, add 2 mlacetonitrile to 0.1 g biotin phosphoramidite(M010381-01) or 5ml acetonitrile to 0.25 gbiotin phosphoramidite (M010382-01) toobtain a concentration of 50 mg/ml. For useon ABI instruments, add 1ml acetonitrile to0.1 g biotin phosphoramidite (M010331-01),or, to obtain a concentration of 100 mg/ml,add 2.5 ml acetonitrile to 0.25 g biotinphosphoramidite (M010332-01).


4. Once the biotin phosphoramidite has beendissolved and placed on your instrument, itshould be used within 48 hours. If you do notplan to use all of the material in 48 hours,remove the vial, seal carefully and store at –20°C until needed.

5. Biotin phosphoramidite is supplied in V-vialsfor the Expedite instrument. A new end-linefilter should be installed prior to placing thephosphoramidite on a Expedite instrument.The tubing length can be shortened bycutting the tubing to fit the V-vial.


7. Enter the sequence of the oligonucleotide youwish to synthesize with biotin phospho -ramidite at the 5'-end. The coupling time forbiotin phosphoramidite is the same as thatrecommended by the instrument manu -facturer for the four standard DNA phospho -ramidites A, C, G and T. Note that the biotinphosphoramidite will terminate the synthesisand can only be employed in the lastcoupling step on the 5' terminus.

8. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending on yourintended further usage of the oligomer, youcan either choose DMT-On, or, DMT-Offprocedures. The coupling efficiency of thebiotin phosphoramidite may be determinedby a standard dimethoxytrityl cation assay.

9. We recommend to elongate the last acidicdeblocking step, for the release of the DMT-group on the biotin moiety, in DMT-Off mode.A deprotection time of 5 minutes is sufficient.

10. Cleave and deprotect the oligonucleotide withammonia at 55°C for 8 hours with standardprotected nucleobases, or, if TAC-protectedphosphoramidites are used, at 55°C for 15minutes. Biotin phosphoramidite from ProligoReagents is compatible with standard andfast deprotection schemes. The biotin moietymaintains its biological activity after it isprocessed using standard workup conditions.

11. The oligonucleotide is now ready for furtherprocessing, such as desalting or purificationwith RP-HPLC, AX-HPLC or gel-based methods.

Biotin PhosphoramiditeChemical Formula C46H64N5O8PS


Storage: ≤-10°C

DMT-Biotin-ß-Cyanoethylphosphoramidite

32


Method

1. Use anhydrous acetonitrile (water content 30ppm) to dissolve the ssH-linker.* It isimportant to maintain anhydrous conditionsduring liquid transfer and dissolution.

2. For use on Expedite instruments, add 5mlacetonitrile to 0.25 g ssH-linker (M010982-01)to obtain a concentration of 50 mg/ml. Foruse on ABI® instruments, add 3.7 mlacetonitrile to 0.25 g ssH-linker (M010932-01)to prepare a 0.1 M solution.

3. The ssH-linker is a viscous oil that requiresmore time to dissolve than powderedphosphoramidites. Gently swirl the vial untilthe linker is completely dissolved.


5. Enter the sequence of the oligonucleotide youwish to synthesize with ssH-linker.

The coupling time for ssH-linker is the sameas that recommended by the instrumentmanufacturer for the four standard DNAphosphoramidites A, C, G and T. Note thatthe ssH-linker will terminate the synthesis andcan only be employed in the last couplingstep on the 5' terminus.

6. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending on yourintended further usage of the oligomer, youcan either choose Trityl-On or Trityl-Offprocedures. The coupling efficiency of thessH-linker may be determined by a mono-methoxytrityl cation assay in Trityl-Off mode.Standard deblock steps as used for theremoval of DMT-groups during oligonucleotidechain assembly can be applied for theremoval of the MMT*-group in Trityl-Off mode.

7. After synthesis in Trityl-Off mode theoligonucleotide is ready for on-supportlabeling. Perform the labeling reaction byincubating the support in the respectivereaction mixture and wash the supportappropriately.**

8. Cleave and deprotect the oligonucleotide with ammonia at 40°C for 24 hours withstandard protected nucleobases, or, if TAC-protected phosphoramidites are used, at 55°C for 15 minutes.

9. The oligonucleotide is now ready for furtherprocessing, such as desalting or purificationwith RP-HPLC, AX-HPLC or gel-basedmethods. MMT-protected ssH-linkeroligonucleosides are particularly suitable forcartridge-based reverse phase purification.

10. Oligonucleotides prepared in Trityl-On modeare further deprotected by a treatment with10% aqueous acetic acid for 20 minutes atroom temperature. Acetic acid is removed byevaporation under vacuum. Free MMTresidues can be removed, if desired, byextraction of an aqueous solution of theoligonucleotide with diethyl ether.

* monomethoxytrityl

** During oligonucleotide deprotection in ammonia the amino groupshould either be MMT-protected or conjugated to a reportergroup. Unprotected amino groups will react with the internalcarbamate linkage under deprotection conditions resulting in aderivative which is unreactive to common labeling reagents.

ssH-LinkerChemical Formula: C38H53N4O5P

Formula Weight : 676,83

Storage : ≤-10°C

33

Method

1. Use anhydrous acetonitrile (water content ≤30ppm) to dissolve the MMT-amino linkerphosphoramidite. It is important to maintainanhydrous conditions when dissolving thelinker compound in acetonitrile.

2. For use on Expedite instruments, add 5mlacetonitrile to 0.25 g MMT-amino linkerphosphoramidite (M010282-01) to obtain aconcentration of 50 mg/ml. For use on ABIinstruments, add 4.2 ml acetonitrile to 0.25 gMMT-amino linker phosphoramidite(M010232-01) to prepare a 0.1 M solution.

3. The MMT-amino linker phosphoramidite is aviscous oil that requires more time to dissolvethan powdered phosphoramidites. Gently swirlthe vial until the linker is completely dissolved.


5. Enter the sequence of the oligonucleotide youwish to synthesize with MMT-amino linkerphosphoramidite. The coupling time for MMT-amino linker phosphoramidite is the same asthat recommended by the instrumentmanufacturer for the four standard DNAphosphoramidites A, C, G and T. Note that theMMT-amino linker phosphoramidite will terminatethe synthesis and can only be employed in thelast coupling step on the 5' terminus.

6. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending on yourintended further usage of the oligomer, youcan either choose Trityl-On, or, Trityl-Offprocedures. The coupling efficiency of theMMT-amino linker phosphoramidite may bedetermined by a monomethoxytrityl cationassay in Trityl-Off mode.

7. We recommend to elongate the last acidicdeblocking step, for the release of the MMT-group on the amino linker, in Trityl-Off mode.A deprotection time of 5 minutes is sufficient.

8. Upon synthesis in Trityl-Off mode, treat theCPG-bound oligonucleotide with an excess ofa 10% solution of triethylamine in acetonitrilefor 10 minutes at room temperature and washwith acetonitrile. This procedure cleaves thecyanoethyl-protective groups from thephosphate moieties of the oligonucleotideand prevents side-reactions arising from thealkylation of the primary amine.

9. Cleave and deprotect the oligonucleotide with ammonia at 40°C for 24 hours withstandard protected nucleobases, or, if TAC-protected phosphoramidites are used, at 55°C for 15 minutes.

10. The oligonucleotide is now ready for furtherpro cessing, such as desalting or purificationwith RP-HPLC, AX-HPLC or gel-basedmethods. Cartridge-based reverse phasemethods are suitable for oligonucleotidesprepared with the MMT-amino linkerphosphoramidite in Trityl-On mode.

11. Oligonucleotides prepared in Trityl-On modeare further deprotected by a treatment with80% acetic acid for 3 hours at roomtemperature. Acetic acid is removed byvacuum centrifugation. Free MMT residuescan be removed, if desired, by extraction ofan aqueous solution of the oligonucleotidewith diethyl ether.

MMT-Amino Linker PhosphoramiditeChemical Formula: C35H48N3O3P


Storage: ≤-10°C

MMT-Aminohexanol-ß-Cyanoethylphosphoramidite

34


Method

1. Use anhydrous acetonitrile (water content ≤30ppm) to dissolve the TFA-amino linkerphosphoramidite. It is important to maintainanhydrous conditions when dissolving thelinker compound in acetonitrile.

2. For use on Expedite instruments, add 5 mlacetonitrile to 0.25 g TFA-amino linkerphosphoramidite (M010682-01) to obtain aconcentration of 50 mg/ml. For use on ABIinstruments, add 6.3ml acetonitrile to 0.25 gTFA-amino linker phosphoramidite (M010632-01) to prepare a 0.1 M solution.

3. The TFA-amino linker phosphoramidite is aviscous oil that requires more time to dissolvethan powdered phosphoramidites. Gently swirlthe vial until the linker is completely dissolved.


5. Enter the sequence of the oligonucleotide youwish to synthesize with the TFA-amino linkerphosphoramidite. The coupling time for theTFA-amino linker phosphoramidite is thesame as that recommended by the instru mentmanufacturer for the four standard DNAphosphoramidites A, C, G and T. Note that theTFA-amino linker phosphoramidite will terminatethe synthesis and can only be employed in thelast coupling step on the 5' terminus.

6. Proceed as you would with a standard DNA oligonucleotide synthesis using theTrityl-OFF mode.

7. Treat the CPG-bound oligonucleotide with anexcess of a 10% solution of triethylamine inacetonitrile for 10 minutes at room temperatureand wash with acetonitrile. This procedurecleaves the cyanoethyl-protective groups fromthe phosphate moieties of the oligonucleotideand prevents side-reactions arising from thealkylation of the primary amine.

8. Cleave and deprotect the oligonucleotide withammonia at 55°C for 8 hours with standardprotected nucleobases. If the conventionalisobutyryl (ib) protective group on dG isreplaced with the dimethylformamidine (dmf)group, a shorter deprotection time of 2 hoursat 55°C may be used.

9. The oligonucleotide is now ready for furtherprocessing, such as desalting or purificationwith RP-HPLC, AX-HPLC or gel-basedmethods. Note that cartridge-based reversephase methods are not suitable for oligo -nucleotides prepared with the TFA-aminolinker phosphoramidite.

TFA-Pentylamino Linker PhosphoramiditeChemical Formula: C16H29F3N3O3P


Storage: ≤-20°C

Trifluoroacetyl-Aminopentanol-ß-Cyanoethylphosphoramidite

TFA-Hexylamino Linker PhosphoramiditeChemical Formula: C17H31F3N3O3P


Storage: ≤-20°C

Trifluoroacetyl-Aminohexanol-ß-Cyanoethylphosphoramidite

35

Method

1. Use anhydrous acetonitrile (water content ≤30ppm) as diluent. It is important to maintainanhydrous conditions while dissolvingdeoxyuridine phosphoramidite in acetonitrile.

2. For use on Expedite instruments, add 5mlacetonitrile to 0.25 g deoxyuridinephosphoramidite (M110281-01) to obtain aconcentration of 50 mg/ml. For use on ABIinstruments, add 3.4 ml acetonitrile to 0.25 gdeoxyuridine phosphoramidite (M110231-01)to prepare a 0.1 M solution.


4. Attach the dissolved phosphoramidite to anappropriate position on the synthesizer.Ensure that the delivery line to the synthesischamber is sufficiently primed.

5. Enter the sequence of the oligonucleotide youwish to synthesize with deoxyuridinephosphoramidite. The coupling time fordeoxyuridine phosphoramidite is the same as that recommended by the instrumentmanufacturer for the four standard DNAphosphoramidites A, C, G and T.

6. Proceed as you would with a standard DNAoligonucleotide synthesis.

7. Cleave and deprotect the oligonucleotide withammonia at 55°C for 8 hours with standardprotected nucleobases, or, if TAC-protectedamidites are applied, at 55°C for 15 minutes. Deoxyuridine phosphoramiditefrom Proligo Reagents is compatible withstandard and fast deprotection schemes,including methylamine-derived deprotectionagents such as AMA.

8. The oligonucleotide is now ready for furtherprocessing such as desalting or purificationwith RP-HPLC, AX-HPLC or gel-based methods.

Non-Standard Nucleosides

Several applications of synthetic oligonucleotides

are based on nucleosides with alternative

heterocycles. SAFC Supply Solutions provides

phosphoramidites of selected non-standard

nucleosides as catalog items and offers custom

synthesis services for proprietary monomers.

Non-Standard Nucleosides

Deoxyuridine PhosphoramiditeChemical Formula: C39H47N4O8P


Storage: ≤+10°C

DMT-Deoxyuridine-ß-Cyanoethylphosphoramidite

N

OO

O

OCH3

CH3O

HN

O

PO

CN

N

O

Non-Standard NucleosidesCompatible with Expedite and Polygen Instruments


M113381-01 5-Methyl-dC(ac) Amidite 1 x 0.25 g

M111181-01 DMT-dInosine Amidite 1 x 0.25 g

M110281-01 DMT-dUridine Amidite 1 x 0.25 g





36

Products Non-Standard Nucleosides

7. For oligonucleotides with a high content ofdeoxyinosine, we recommend to treat theCPG-bound oligonucleotide with an excess ofa 10% solution of triethylamine in acetonitrilefor 10 minutes at room temperature, followedby washing with acetonitrile. This procedurecleaves the cyanoethyl-protecting groupsfrom the phosphate moieties of theoligonucleotide and prevents minor side-reactions arising from the alkylation of thebase of deoxyinosine phosphoramidite.

8. Otherwise, cleave and deprotect the oligo -nucleotide with ammonia at 55°C for 8 hourswith standard protected nucleobases, or, ifTAC-protected phosphoramidites are used, at55°C for 15 minutes. Our Deoxyinosine phos -phoramidite is com patible with standard andfast deprotection chemistries, includingmethylamine-derived deprotection agentssuch as AMA.


Method

1. Use anhydrous acetonitrile (water content ≤30ppm) to dissolve the deoxyinosinephosphoramidite. It is important to maintainanhydrous conditions when dissolving thedeoxyinosine phosphoramidite in acetonitrile.

2. For use on Expedite instruments, add 5 mlacetonitrile to 0.25 g deoxyinosine phos -phoramidite (M111181-01) to obtain aconcentration of 50 mg/ml. For use on ABIinstruments, add 3.3 ml acetonitrile to 0.25 gdeoxyinosine phosphoramidite (M111131-01)to prepare a 0.1 M solution.



5. Enter the sequence of the oligonucleotideyou wish to synthesize with deoxyinosinephosphoramidite. The coupling time fordeoxyinosine phosphoramidite is the sameas that recommended by the instrumentmanufacturer for the four standard DNAphosphoramidites A, C, G and T.


Deoxyinosine PhosphoramiditeChemical Formula: C40H47N6O7P


Storage: ≤+10°C

DMT-Deoxyinosine-ß-Cyanoethylphosphoramidite

N

NH

N

N

OO

O

OCH3

CH3O

PO

CNN

O

37

Method

1. Use anhydrous acetonitrile (water content ≤30ppm) to dissolve the 5-methyl-dC(ac)phosphoramidite. It is important to maintainanhydrous conditions when dissolving the 5-methyl-dC(ac) phosphoramidite in acetonitrile.

2. For use on Expedite instruments, add 5 mlacetonitrile to 0.25 g 5-methyl-dC(ac) phos -pho ramidite (M113381-01) to obtain a con -centration of 50 mg/ml. For use on ABIinstruments, add 3.2 ml acetonitrile to 0.25 g5-methyl-dC(ac) phosphoramidite (M113331-01)to prepare a 0.1 M solution.



5. Enter the sequence of the oligonucleotide youwish to synthesize with 5-methyl-dC(ac) phos -phoramidite. The coupling time for 5-methyl-dC(ac) phosphoramidite is the same as that

recommended by the instrumentmanufacturer for the four standard DNAphosphoramidites A, C, G and T.


7. Cleave and deprotect the oligonucleotide withammonia at 55°C for 8 hours with standardprotected nucleobases, or, if TAC-protectedphosphoramidites are used, at 55°C for 15minutes. 5-methyl-dC(ac) phosphoramiditefrom Proligo Reagents is compatible withstandard and fast deprotection chemistries,including methylamine-derived deprotectionagents such as AMA.


5-Methyl-dC(ac) PhosphoramiditeChemical Formula: C42H52N5O8P


Storage: ≤-20°C

DMT-5-Methyl-Deoxycytidine(ac)-ß-Cyanoethylphosphoramidite

N

OO

O

OCH3

CH3O

N

O

HN

O

PO

CN

N

CH3

CH3

38

Products

Phosphate-ON Phosphoramidite

Phosphate-ON phosphoramidite is a chemical

phosphorylation reagent that can be employed to

introduce a phosphate group at the 5' terminus

of an oligonucleotide. Chemical phosphorylation

is a cost-effective alternative to enzymatic

phosphorylation methods, allowing introduction

of terminal phosphate groups in high yields, at

any desired scale.

SAFC Supply Solutions’ Proligo® Reagents offersPhosphate-ON phospho ramidite in powder form,enabling the dissolution of the reagent in acetonitrileto be easily monitored. The application of thereagent is fully compatible with standard cleavageand deprotection procedures at the end of oligo -nucleotide synthesis. Our phosphate-ONphosphoramidite comprises a thymidine nucleoside,which is removed from the oligonucleotide duringthe cleavage and deprotection process.

Key Features of 5'-PhosphorylatedOligonucleotides

• Enables enzymatic ligation to the 3'-terminus ofnucleic acids

• Offers protection against exonucleolyticdegradation

• Provides oligonucleotide conjugation throughactivation with coupling reagents such as EDC

These features enable 5'-phosphorylated oligo -nucleotides to be used in applications such asmolecular cloning and gene construction; ligasechain reaction; template directed ligation; oligo -nucleotide labeling with reporter groups, haptensand other modifiers; and oligonucleotide stabilization.

Key Features of Phosphate-ONPhosphoramidite

• Fully compatible with standard phospho -ramidite reagents and synthesis conditions

• Compatible with dG(dmf) fast deprotectionchemistry: the oligonucleotide can be cleavedfrom the support and deprotected in con -centrated ammonia at 55°C in only 2 hours

• Comprises a DMT-group for trityl monitoring

• Dissolves easily in acetonitrile to a 0.1 M solution

• Powder format enables dissolution to be easilymonitored and facilitates product handling

• High coupling efficiency of ≥98.0% under stan dardDNA phosphoramidite coupling conditions

• Cleavage of both phosphate protective groupsthrough a ß-elimination process

Phosphate-ON Phosphoramidite

Phosphate-ON PhosphoramiditeCompatible with Expedite and Polygen Instruments


M010782-01 Phosphate-ON Amidite 1 x 0.25 g



Other quantities available upon request.

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/phosphateon-phosphoramidite.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

39

Method

1. Use anhydrous acetonitrile (water content ≤30ppm) as diluent. It is important to maintainanhydrous conditions while dissolvingphosphate-ON phosphoramidite inacetonitrile.

2. For use on Expedite instruments, add 5 mlacetonitrile to 0.25 g phosphate-ON phos -phoramidite (M010782-01) to obtain aconcentration of 50 mg/ml. For use on ABIinstruments, add 2.5 ml acetonitrile to 0.25 gphosphate-ON phosphoramidite (M010732-01)to obtain a concentration of 100 mg/ml.


4. Once the phosphate-ON phosphoramiditehas been dissolved and placed on yourinstrument, it should be used within 4 days. If you do not plan to use all of the material in4 days, remove the vial, seal carefully, andstore at –20°C until needed.


6. Enter the sequence of the oligonucleotideyou wish to synthesize with a phosphategroup at the 5'-end. The coupling time forphosphate-ON phosphoramidite is the sameas that recommended by the instrumentmanufacturer for the four standard DNAphosphoramidites A, C, G and T.

7. The phosphate-ON phosphoramidite isdesigned for the phosphorylation of the 5'-endof the oligonucleotide and should only beemployed in the last coupling step.

8. Proceed as you would with a standard DNAoligonucleotide synthesis. Depending on yourfurther use of the oligomer, you can eitherchoose DMT-On or DMT-Off procedures. Thecoupling efficiency of the phosphate-ONphosphoramidite may be determined by astandard dimethoxytrityl cation assay.

9. Cleave and deprotect the oligonucleotide withammonia at 55°C for a minimum time of 2hours. Our phosphate-ON phosphoramidite iscompatible with a variety of deprotectionconditions and base-protection schemes,including standard protective groups (ammoniafor 8 hours at 55°C), the incorporation ofdimethyl forma midine (dmf) protected guanidinemonomers (ammonia for 2 hours at 55°C), andthe incorporation of tert-butyl phe noxy acetyl(TAC) protected cytidine monomers (AMAreagent for 10 minutes at 65°C). If the DMT-Onmodus is used, the DMT group will be removedduring the final cleavage and deprotection step.


Phosphate-ON PhosphoramiditeChemical Formula: C49H62N7O11P


Storage: ≤-10°C

40

Products NPPOC Phosphoramidites

NPPOC Phosphoramidites

Phosphoramidites with a NPPOC 5'-protection

group can be used for the production of DNA

microarrays using photolithographic in situ

synthesis of oligonucleotides directly on the

chip. This method offers the possibility to

produce DNA chips of extremely high density

and provides a flexible system.

Features of NPPOC Chemistry:

• Efficient photolytic deprotection (> 99%)

• Less side products during photolysis

• Products available

• Lot-to-lot consistent high purity andperformance


Analytical Specifications

Please ask for delivery dates of these specialty amidites.

Test A C G THPLC Purity ≥96.0% ≥96.0% ≥96.0% ≥96.0%

31P-NMR ≥96% ≥96% ≥96% ≥96%

NPPOC-dA(tac) Amidite

HN

N

N

N

O

N

OP

NO

CN

O

O

O O

O

NO2

NPPOC-dC(ib) Amidite

OO

N

N

HN

O

OP

NO

CN

O

O

O

NO2

NPPOC-dG(ipac) Amidite

O

O

NO2

N

N

NH

O

OO

N

OP

NO

CN

NH

O

O

NPPOC-dT Amidite

O

N

HN

O

O

OP

NO

CN

O O

O

NO2

NPPOC PhosphoramiditesCatalog No. Description Unit

A112N01-01 NPPOC-dA(tac) Amidite 1 x 1 g

C114N01-01 NPPOC-dC(ib) Amidite 1 x 1 g

G114N01-01 NPPOC-dG(ipac) Amidite 1 x 1 g

T111N01-01 NPPOC-dT Amidite 1 x 1 g

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/new-proligo-reagents.html#nppoc?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

41

User Instructions

1. Liquid Reagents

Deblock — The NPPOC-protective group isremoved with light while the support-anchoredoligonucleotide is immersed in a liquid reagent;various formulations are applicable, our recom -mended formulations are 1% NMI in DMSO (v/v) or1% NMI in ACN (v/v) Activator — Any commercialactivator that works for DNA-amidites is applicable;0.25 M DCI in ACN is perfect

Oxidizer — Although any commercial oxidizer isapplicable some customers use flow cells that areincompatible with THF and therefore prefer to use anoxidizer wherein the solvent THF is replaced by ACN

Cap A — Fast Cap A is recommended (TAC-anhydride solution); some customers use flow cellsthat are incompatible with THF and therefore preferto use a Cap A reagent wherein the solvent THF isreplaced by ACN; some customers do not employcapping steps with NPPOC-chemistry

Cap B — Cap B solutions that are compatible withFast Cap A; some customers use flow cells thatare incompatible with THF and therefore prefer touse a Cap B reagent wherein the solvent THF isreplaced by ACN

2. Coupling

NPPOC-amidites are dissolved in ACN at theconcentration recommended for standard DNAamidites by the manufacturer of the DNA/RNAsynthesizer. The coupling times of NPPOC-Amidites match the coupling times of standardDNA amidites (30 to 60 sec., longer coupling timesare applicable, but not necessary).

3. Deprotection of NPPOC-groups

Light with a wavelength between 350 and 390 nm isapplicable. The deprotection time depends on thelight intensity. 90 sec. illumination time is sufficientat 100 mW/cm2 on the surface of the synthesissupport (365 nm Hg/Xe high pressure lamp).

4. Deprotection of base protective groups

Any fast deprotection protocol (e.g., conc.ammonia/room temp./2 hours or AMA/roomtemp./30 min.) is applicable. However, suchtreatment will partly remove the oligonucleotidesfrom silica surfaces and therefore a mildertreatment with a mixture of ethylendiamine andethanol 50/50, v/v, for 2 hours at room temperatureis used as an industry standard.

42

Products Controlled Pore Glass and Columns — CPG Free Flow

Controlled Pore Glass

Since Professor Merrifield first described solid

phase synthesis, researchers have investigated

numerous supports for the chemical synthesis

of DNA. Controlled Pore Glass (CPG) has

proven to be the most accepted standard, with

features such as high surface area, efficient

mass transfer and chemical inertness.

Because the pore density of CPG can be adjusted,the solid support can be tailored to the size of thesynthetic oligonucleotide required. Bigger poresize is typically preferable in minimizing stericeffects during the synthesis of long oligo -nucleotides, while smaller pore size fostersimproved synthesis consistency.

Our process guarantees consistent production ofCPGs to specifications designed for DNA synthesis.

All products are tested in our Quality Control labsfor purity and identity prior to release.

Analytical Parameters of CPGCPG (UHL) CPG 500Å CPG 1000Å

Pore size (nm) 33 50 100

Pore volume (ml/g) 1.3 1.0 1.3

Grain size (�m) 100–180 100–180 100 –180

Surface (m2/g) ~100 ~60 ~30

Nucleoside-Loaded CPG

Loading �mol/g

CPG 500Å 30–40

CPG 1000Å 25–35

CPG UHL 50–70

CPG UHL 90–110

DNA CPGCatalog No. Description Unit

A301001-01 CPG 500Å dA(bz), 30-40 �mol/g 1 x 1 g

C301001-01 CPG 500Å dC(bz), 30-40 �mol/g 1 x 1 g

G301001-01 CPG 500Å dG(ib), 30-40 �mol/g 1 x 1 g

T301001-01 CPG 500Å dT 30-40 �mol/g 1 x 1 g




T301010-01 CPG 500Å dT 30-40 �mol/g 1 x 10 g




T401001-01 CPG 1000Å dT 25-35 �mol/g 1 x 1 g




T401010-01 CPG 1000Å dT 25-35 �mol/g 1 x 10 g

Fast Deprotection CPGCatalog No. Description Unit

C303001-01 CPG 500Å dC(ac) 30-40 �mol/g 1 x 1 g




A302001-01 CPG 500Å dA(tac), 30-40 �mol/g 1 x 1 g

C302001-01 CPG 500Å dC(tac), 30-40 �mol/g 1 x 1 g

G302001-01 CPG 500Å dG(tac), 30-40 �mol/g 1 x 1 g






G305001-01 CPG 500Å dG(dmf), 30-40 �mol/g 1 x 1 g


Fast Deprotection RNA CPGCatalog No. Description Unit

A602001-01 CPG 500Å rA(tac), 25-35 �mol/g 1 x 1 g

C602001-01 CPG 500Å rC(tac), 25-35 �mol/g 1 x 1 g

G602001-01 CPG 500Å rG(tac), 25-35 �mol/g 1 x 1 g

U601001-01 CPG 500Å rU, 25-35 �mol/g 1 x 1 g

2’0-Methyl RNA CPGCatalog No. Description Unit

A601101-01 CPG 500Å 2'O-Methyl-rA(bz), 30-40 �mol/g 1 x 1 g

C602101-01 CPG 500Å 2'O-Methyl-rC(tac), 30-40 �mol/g 1 x 1 g

G601101-01 CPG 500Å 2'O-Methyl-rG(ib), 30-40 �mol/g 1 x 1 g

U601101-01 CPG 500Å 2'O-Methyl-rU, 30-40 �mol/g 1 x 1 g


CPG-products can be provided with higherloadings based on UHL-CPG (50–70 �mol/g or9 0 –110 �mol/g), please inquire.

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/controlled-pore-glass-columns.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

43

Columns for Synthesizers

Columns for Synthesizers

In addition to our CPG free flow oligonucleotide

synthesis supports, we offer ready to use

synthesis columns filled with CPG or polystyrene

support. These columns are designed for use on

a wide range of synthesizers for high quality

oligonucleotide synthesis. Our columns are

produced at our high quality standard in order

to be compliant in the required application and

compatible with standard synthesis protocols.

Expedite columns

• Filled with CPG 500Å and CPG 1000Å

• For Expedite 89er series only

• Crimped

• Color coded label

Cyclopeadic columns for ABI andExpedite synthesizer


• Available in 50 nmol, 0.2 �mol and 1 �mol

• No leakage (no crimping)

• One column body

• Color coded body, limits the wrong use of basein synthesis

Columns for ABI 3900 synthesizers

• Filled with Polystyrene

• For ABI 3900 synthesizers only

• Available in 40 nmol, 0,2 �mol

• Polystyrene 40 is comparable with CPG 1000Å

• Color coded body, limits the wrong use of basein synthesis

RNA columns for ABI synthesizers

• Filled with CPG 500Å

• For ABI 39X/3400 synthesizers only

• Crimped


RNA columns for Expedite synthesizers


• For ABI 39X/3400 synthesizers only

• Crimped


DNA ColumnsCompatible with Expedite Instruments


A311010-01 Column CPG 500Å dA(bz), 50 nmol 1 x 100

C311010-01 Column CPG 500Å dC(bz), 50 nmol 1 x 100

G311010-01 Column CPG 500Å dG(ib), 50 nmol 1 x 100

T311010-01 Column CPG 500Å dT, 50 nmol 1 x 100

A321010-01 Column CPG 500Å dA(bz), 0.2 �mol 1 x 100

C321010-01 Column CPG 500Å dC(bz), 0.2 �mol 1 x 100

G321010-01 Column CPG 500Å dG(ib), 0.2 �mol 1 x 100

T321010-01 Column CPG 500Å dT, 0.2 �mol 1 x 100

A331010-01 Column CPG 500Å dA(bz), 1 �mol 1 x 100

C331010-01 Column CPG 500Å dC(bz), 1 �mol 1 x 100

G331010-01 Column CPG 500Å dG(ib), 1 �mol 1 x 100

T331010-01 Column CPG 500Å dT, 1 �mol 1 x 100









Compatible with Expedite & ABI Instruments

A341010-01 Column CPG 500Å dA(bz), 50 nmol, ABI/89 1 x 100

C341010-01 Column CPG 500Å dC(bz), 50 nmol, ABI/89 1 x 100

G341010-01 Column CPG 500Å dG(ib), 50 nmol, ABI/89 1 x 100

T341010-01 Column CPG 500Å dT, 50 nmol, ABI/89 1 x 100

A351010-01 Column CPG 500Å dA(bz), 0.2 �mol, ABI/89 1 x 100

C351010-01 Column CPG 500Å dC(bz), 0.2 �mol, ABI/89 1 x 100

G351010-01 Column CPG 500Å dG(ib), 0.2 �mol, ABI/89 1 x 100

T351010-01 Column CPG 500Å dT, 0.2 �mol, ABI/89 1 x 100

A361010-01 Column CPG 500Å dA(bz), 1 �mol, ABI/89 1 x 100

C361010-01 Column CPG 500Å dC(bz), 1 �mol, ABI/89 1 x 100

G361010-01 Column CPG 500Å dG(ib), 1 �mol, ABI/89 1 x 100

T361010-01 Column CPG 500Å dT, 1 �mol, ABI/89 1 x 100








T461010-01 Column CPG 1000Å dT 0.2 �mol, ABI/89 1 x 100

44

Products Columns for Synthesizers

DNA Columns (cont.)Compatible with ABI 3900 Instruments


A911010-01 Column Polystyrene 40 dA(bz), 40 nmol, ABI 3900

1 x 100

C911010-01 Column Polystyrene 40 dC(bz), 40 nmol, ABI 3900

1 x 100

G915010-01 Column Polystyrene 40 dG(dmf), 40 nmol, ABI 3900

1 x 100

T911010-01 Column Polystyrene 40 dT, 40 nmol, ABI 3900 1 x 100

A921010-01 Column Polystyrene 40 dA(bz), 0.2 µmol, ABI 3900

1 x 100

C921010-01 Column Polystyrene 40 dC(bz), 0.2 µmol, ABI 3900

1 x 100

G925010-01 Column Polystyrene 40 dG(dmf), 0.2 µmol, ABI 3900

1 x 100

T921010-01 Column Polystyrene 40 dT, 0.2 µmol, ABI 3900 1 x 100

Fast Deprotection RNA ColumnsCompatible with Expedite Instruments


A632004-01 Column CPG 500Å rA(tac), 1 �mol 1 x 4

C632004-01 Column CPG 500Å rC(tac), 1 �mol 1 x 4

G632004-01 Column CPG 500Å rG(tac), 1 �mol 1 x 4

U631004-01 Column CPG 500Å rU, 1 �mol 1 x 4






2’0-Methyl RNA ColumnsCompatible with Expedite Instruments


A631104-01 Column CPG 500Å 2'O-Me-rA(bz), 1 �mol 1 x 4

C632104-01 Column CPG 500Å 2'O-Me-rC(tac), 1 �mol 1 x 4

G631104-01 Column CPG 500Å 2'O-Me-rG(ib), 1 �mol 1 x 4

U631104-01 Column CPG 500Å 2'O-Me-rU, 1 �mol 1 x 4






45

Amino-ON CPG

Amino-ON CPG can be employed to conjugate

biotin, fluorescein or other modifiers and

reporter groups to the 3'-end of oligo nu cle otides

or to attach oligonucleotides to surfaces. SAFC

Supply Solutions’ Proligo Reagents Amino-ON

CPG combines the advanced features of

cleavage and deprotection under mild

conditions, and maintenance of the integrity of

the 3'-modification with high synthesis yields.

Key Features of 3'-AmineOligonucleotides

• Selective conjugation to reporter groups,purification handles or other modifiers

• 3'-end attachment to electrophilic surfaces

• Offers protection against exonucleolyticdegradation

These features enable 3'-Amine oligonucleotides tobe used in applications such as 3'-labeling withbase sensitive dyes; 3'-biotin modifications; dual-labeled probes (eg TaqMan probes and Molecularbeacons); and microarray spotting.

Key Features of Amino-ON CPG

• Introduces a primary amino group attached to aC6-linker

• Fully compatible with standard phospho -ramidite reagents and synthesis conditions

• Can be used with DNA, RNA and Locked NucleicAcid® (LNA); 5'-oligonucleotide modificationssuch as fluorescein or biotin; and with thesynthesis of thioated DNA oligonucleotides

• Compatible with dG(dmf) fast deprotectionchemistry: the oligonucleotide can be cleavedfrom the support and deprotected in con -centrated ammonia at 55°C in 2 hours

• Provides all the advantages of homogeneouspore size porous glass supports

• Standard pore size of 500Å

• Loading of 30–40 �mol/g

• Coupling performance of ≥99.0% stepwise efficiency

• DMT-protected in the same way as standardnucleoside-loaded CPG

Amino-ON CPG

Amino-ON CPGBulk CPG


M020101-01 Amino-ON CPG 500Å, 30-40 �mol/g 1 x 0.25 g

M020111-01 Amino-ON CPG 500Å, 30-40 �mol/g 1 x 1 g

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/aminoon-cpg.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

46

Products Amino-ON CPG

SAFC Supply Solutions’ Proligo Reagents Amino-ONCPG can be employed to introduce a covalentlybound, primary amino group at the 3'-end of anyoligonucleotide. Amino-ON CPG comprises aprotected hexylamino group. The free amine isliberated under the alkaline conditions that areemployed to cleave and deprotect the oligonucleotideon the support, while the hexylamino group remainsattached to the oligonucleotide. The amino-ON CPGfurther comprises a DMT-protective group, which isremoved in the first synthesis cycle similar to the DMT-group of standard nucleoside loaded CPG.

The synthesis of oligonucleotides is conducted inthe same manner as with nucleoside-loaded CPG,without changes in any of the reagents of thesynthesis. The only differences in the preparationof oligonucleotides using Proligo Reagents’ amino-ON CPG are as follows:

• the 3'-base of the oligonucleotide to besynthesized is not attached to the support: thisbase must be added in the first synthesis cycle

• there is a simple modification to the cleavageand deprotection conditions, as detailed below

Amino-ON CPG can be employed in the samemanner to prepare 3'-amino DNA, RNA, LNA or2’O-Methyl oligonucleotides. It can be applied with5'-biotin, fluorescein and other oligonucleotidemodifications, and for the synthesis of thioatedDNA oligonucleotides.

Proligo Reagents offers amino-ON CPG in bulk,with a pore size of 500Å.

Cleavage and deprotection

The cleavage and deprotection of oligonucleotideson amino-ON CPG can be performed with a varietyof reagents. We have successfully applied thefollowing reagents and conditions to simul -taneously deprotect the hexylamino group and theoligonucleotide:

• concentrated ammonia at 55°C for 2 hours or

• 40% aqueous methylamine/concentratedammonia 1/1, v/v, at 65°C for 10 minutes

Method

1. Attach the amino-ON CPG to the synthesizerin the same way as a nucleoside loaded CPG.

2. Enter the sequence of the oligonucleotide youwish to synthesize. Note that the 3'-nucleosideof the oligonucleotide sequence must beincluded in the bases to be attached to thesupport during the synthesis. This can beachieved with a dummy nucleoside unit for the3'-end of the sequence, e.g., add a thymidineunit to the 3'-end of the sequence.

3. Proceed as you would with a standardoligonucleotide synthesis. Depending on yourintended further use of the oligomer you caneither choose DMT-On or DMT-Off procedures.

4. The first deblocking step proceeds with theusual release of the orange colour of thedimethoxytrityl cation and may be utilized intrityl monitoring procedures.

5. Cleave and deprotect the oligonucleotide onthe support using one of the conditions listedunder “Cleavage and deprotection” above.

6. Transfer the supernatant solution of theoligonucleotide from the support into aseparate vial. The yield of the oligonucleotidecan be further improved by rinsing thesupport with water and combining theoligonucleotide solution with the washingsolution. Evaporate to dryness.


Amino-ON CPG 500ÅLoading 30-40 �mol/g

Storage: ≤-10°C

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/aminoon-cpg.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

47

Universal CPG

Universal CPG

Universal CPG from SAFC Supply Solutions

can be employed in the synthesis of any

oligonucleotide sequence instead of

conventional nucleoside loaded CPG —

whether loaded with adenosine, cytidine,

guanosine or thymidine nucleosides. The use

of universal CPG releases your resources as

the purchase, handling and storage of

differentially loaded types of nucleoside-CPG

is not required, eliminating 3'-end synthesis

errors, because of accidental interchange of

polymeric supports.

Key Features of Universal CPG

Fully compatible with standard phosphoramiditereagents and synthesis conditions

Can be employed in the synthesis of manydifferent types of oligonucleotides:

• DNA oligonucleotides

• Phosphorothioates

• 2'O-Methyl oligonucleotides

• Fluorescein, tetrachloro-fluorescein and biotin modifications

• Particularly useful for high-throughputoligonucleotide synthesis

• Coupling efficiency of ≥99.0% is routinely obtained

• Convenient cleavage and deprotection

• Avoids the use of unusual and potentiallyharmful reagents in the deprotection processe.g., heavy metals, sulfides

Universal CPGCatalog No. Description Unit

M301001-01 Universal CPG 500Å, 30-40 �mol/g 1 x 1 g



M401010-01 Universal CPG 1000Å dT 25-35 � mol/g 1 x 10 g

Universal CPGUniversal CPG 500Å Loading 30-40 �mol/g

Universal CPG 1000Å Loading 25-35 �mol/g

Storage: ≤+ 10°C

OO

N

NH

N

N

OO

O

OCH3

N

O

S p ac e r

CPG

H

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/universal-cpg.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf


Universal CPG

48

Products

Our universal CPG can be employed instead ofconventional nucleoside-loaded CPG — whetherloaded with adenosine, cytidine, guanosine orthymidine nucleosides, in the synthesis of anyoligonucleotide sequence, irrespective of the 3'-end nucleoside. The universal CPG contains aninosine-ribonucleotide adapter that is removedfrom the synthesized oligo nucleotide during thecleavage and deprotection reaction.

SAFC’s universal CPG can be used with the samestandard conditions and reagents that are employedfor the synthesis of oligonucleotides conducted withnucleoside-loaded CPG. The preparation differencesof oligonucleotides using our universal CPG, are:

• the 3'-base of the oligonucleotide to besynthesized is not attached to the support: thisbase must be added in the first synthesis cycleon the universal support

• there is a simple modification to the cleavageand deprotection conditions, as detailed below

• the first deblocking step — which is conductedin the usual manner — will not result in therelease of the colored dimethoxytrityl cationfrom the support. This is because the inosine-ribonucleotide adapter contains a different acid-labile protective group (methoxyethylidene group)

The universal CPG can be substituted for allconventional DNA supports, as well as supportsloaded with 2'O-Methyl nucleosides and supportswith other modified nucleosides. It can also beused with biotin and fluorescein phosphoramiditesto produce 3'-modified oligonucleotides, and forthe synthesis of thioated DNA oligonucleotides.

Note: The use of universal CPG for the synthesis ofRNA oligonucleotides or for any synthesis thatinvolves base-labile nucleosides or other base-labile modifications, e.g., rhodamine dyes orCy™3/Cy5, is not recommended.

Cleavage and deprotection

The cleavage of oligonucleotides from theuniversal CPG-support and the deprotectionreaction can be performed with a variety ofreagents. We have successfully applied thefollowing reagents and conditions to completelycleave the inosine-ribonucleotide adapter from theoligonucleotide while simultaneously deprotectingthe oligonucleotide:

• concentrated ammonia/0.5 M lithium chloridesolution 5/1, v/v, at 75°C for 6 hours

• concentrated ammonia/0.5 M sodium chloridesolution 5/1, v/v, at 75°C for 6 hours, or

• 40% aqueous methylamine at 75°C for 6 hours

Method

1. Attach the universal CPG to the synthesizer inthe same way as a nucleoside-loaded CPG.

2. Enter the sequence of the oligonucleotide youwish to synthesize. Note that the 3'-nucleosideof the oligonucleotide sequence must beincluded in the bases to be attached to thesupport during the synthesis. This can beachieved with a dummy nucleoside unit forthe 3'-end of the sequence, e.g., add athymidine unit to the 3'-end of the sequence.

3. Proceed as you would with a standard oligo -nucleotide synthesis. Depending on yourintended further use of the oligomer, you caneither choose DMT-On or DMT-Off procedures.

4. The first deblocking step proceeds withoutrelease of the orange color of thedimethoxytrityl cation. This step isnevertheless necessary to deprotect theinosine-ribonucleoside adapter of theuniversal CPG.

5. Cleave and deprotect the oligonucleotide onthe support using one of the conditions listedunder “Cleavage and deprotection” above.

6. Transfer the supernatant solution of theoligonucleotide from the support into aseparate vial. The yield of the oligonucleotidecan be further improved by rinsing thesupport with water and combining theoligonucleotide solution with the washingsolution. Evaporate to dryness.



49

Liquid Reagents

In solid-phase synthesis of oligonucleotides,

liquid reagents are used in each step of the

synthesis cycle. Overall synthesis performance,

and therefore total product yield and purity of

the crude oligonucleotide, is highly dependent

on the chemical purity of the monomers and the

supporting liquid reagents.

SAFC Supply Solutions has more than 25 years ofmanufacturing experience in DNA and RNAsynthesis reagents. Our liquid reagents meet themost stringent quality specifications, making themideal for use in automated nucleic acid synthesis.Lot-to-lot consistency is guaranteed for everyproduct manufactured in our ISO 9001 certifiedsite. Each lot is individually quality-controlled toensure optimum synthesis performance.

Liquid Reagents

Features Benefits

• Products designedfor oligonucleotidesynthesis

• Constant highsynthesisperformance

• Liquid reagentsoffered in additionto amidites andsupports

• Key oligonucleotidesynthesis reagentsavailable in one shop

• Constant highquality

• Matching with highquality amidites andsupport products

• Broad range ofpackaging

• Offering highflexibility

• Customizedformulations andspecifications

• Special requirements will be fulfilled

• Technical expertise •Supportingcustomized solutions

• New productdevelopment:Activator 42

• Synthesisoptimization and costreduction

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/liquid-reagents.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf


50

Products Liquid Reagents

Chemical Composition and Purpose of Proligo Reagents’ Liquid Reagentsduring the Synthesis Cycle

Deblock solution, containing trichloracetic acid(TCA) or dichloroacetic acid (DCA) in dichloro -methane, removes the dimethoxytrityl (DMT)protecting group from the 5'hydroxyl moiety ofnucleotides already incorporated into the growingnucleic acid, prior to the addition of the nextphosphoramidite. Removal of the DMT allows theunprotected 5'hydroxyl moiety to react with a newphosphoramidite in a subsequent extension reaction.

Wash solution, containing anhydrous acetonitrile(water content ≤30 ppm), is used as the overall washsolvent following each step in the synthesis cycle.

Activator solution, containing powerful activatorslike 4,5-dicyanoimidazole (DCI) or 5-(3,5-bis(trifluoromethyl)phenyl)-1H-tetrazole (Activator 42)in acetonitrile, are mixed with solutions of phospho -ramidites during the extension step. The activatorreacts with the amidite group to form a highlyreactive intermediate. The intermediate then forms aninternucleotide bond with the detritylated 5'hydroxylgroup of the growing oligonucleotide chain.

Cap A solution, containing acetic anhydride andtetrahydrofuran (THF), is used after the phospho -ramidite reaction/coupling step. This solution abortschains bearing unreacted 5'hydroxyl groups due tofailure of reaction with activated phosphoramidite(typically, 1 to 2% of growing oligonucleotide chains

in each synthesis cycle). These unreacted 5'hydroxylgroups are capped with an acetyl group and thusrendered unreactive for subsequent synthesis steps.For synthesis with Proligo Reagents’ TAC-protectedphosphoramidites, Fast Deprotection CAP A solutionmust be employed instead of Cap A solution.

Fast Deprotection Cap A solution must be usedfor synthesis with Proligo Reagents’ TAC-protectedphosphoramidites. Fast Deprotection Cap Asolution, containing tert-butylphenoxyacetyl aceticanhydride (tac2O) in tetrahydrofuran, is used inplace of Cap A solution to ensure that thedisplacement of tert-butylphenoxyacetyl (TAC) onguanine bases of the TAC-protected RNAphosphoramidites does not occur.

Cap B solution, containing tetrahydrofuran (THF),pyridine and N-methylimidazole (NMI), is mixed in situwith Cap A solution during the capping (acetylation)reaction. Pyridine is applied as a mild base while NMIprovides a powerful acylation catalyst.

Oxidizer solution, containing tetrahydrofuran (THF),pyridine, iodine and water, is applied to oxidize thechemically unstable trivalent phosphorous triesterlinkage formed in the coupling reaction to a stablepentavalent phosphate triester. Iodine functions as a mild oxidant and water functions as anoxygen donor.

Activator solution

Capping 1: Cap A and B

solution

Capping 2: Cap A and B

solutions

Oxidation: Oxidizer solution

Detritylation: Deblock solution

Coupling

Start Cycle

Finalized Synthesis: Cleavage and Deprotection after x cycles:

Start of Synthesis*: CPG Column loaded with first nucleoside:

HO

BNBL

O

OO O O O

O

O

O HPP

B

x-1

= =

DMT

B1ac

O OORP

=

O

OO OO

O BLac Bac

x-1

DMT O O P OO

BNac

OR

OO

ORP O= =

BLac

x-1

O

Bac

ORP

=

O

OO OO

O BLac Bac

x-1

DMT O O P OO

BNac

OR

OO

ORP O= =

BLac

x-1

O

Bac

OO

ORP O

=

BLac

x-1

O

Bac

HO

DMT O O P

BNac

OR

N(iPr)2

+

B* = protected baseL = last cycleN = actual new cyclex = number of cycles* = B, is equivalent to BL in the cycle

The Oligonucleotide Synthesis Cycle

For TAC-protected G-amidites (dG(tac) phoshoramidite, rG(tac) phosphoramidite) Fast DeprotectionCap A must be employed to prevent transacylation side reactions on the guanine base.


51

Custom products

Inquire for customized liquid reagents withspecialty formulations or alternative packaging.

Bulk

Packaging in drums or m3-containers is availableupon request.

Liquid ReagentsCatalog No. Description Unit

L010010-06 Amidite Diluent (Acetonitrile) 6 x 100 ml

L010250-04 Acetonitrile 4 x 2.5 L

L010400-04 Acetonitrile 4 x 4 L


L014500-C01-01 Acetonitrile 1 x 45 L



L020250-04 TCA Deblock 4 x 2.5 L

L0202502-04 TFA Deblock Toluene 4 x 2.5 L

L020251-04 DCA Deblock 4 x 2.5 L

L020400-04 TCA Deblock 4 x 4 L


L0302502-04 Activator 42 0.1 M 4 x 2.5 L

L0302512-04 Activator 42 0.25 M 4 x 2.5 L

L0302501-04 ETT Activator 0.25 M 4 x 2.5 L

L040250-01 Cap A 1 x 2.5 L

L040250-04 Cap A 4 x 2.5 L

L040251-01 Cap A for ABI Instruments 1 x 2.5 L

L040400-01 Cap A 1 x 4 L

L050250-01 Cap B 1 x 2.5 L

L050250-04 Cap B 4 x 2.5 L

L050251-01 Cap B for ABI Instruments 1 x 2.5 L

L050400-01 Cap B 1 x 4 L

L060250-04 Oxidizer 0.02 M 4 x 2.5 L

L060251-04 Oxidizer 0.1 M for ABI Instruments 4 x 2.5 L

L060252-04 Oxidizer 0.02 M for ABI 3900 Instruments 4 x 2.5 L

L060400-04 Oxidizer 0.02 M 4 x 4 L

L070250-01 Fast Deprotection Cap A 1 x 2.5 L

L070400-01 Fast Deprotection Cap A 1 x 4 L

L080250-04 DCI Activator 0.25 M 4 x 2.5 L


L080400-04 DCI Activator 0.25 M 4 x 4 L


ACN Based Liquid Reagents

LB40250-01 Cap A ACN 1 x 2.5 L

LB50250-01 Cap B ACN 1 x 2.5 L

LR40250-01 Cap 1 in ACN 1 x 2.5 L

LR50250-01 Fast Deprotection Cap 2 in ACN 1 x 2.5 L

LR60250-04 Oxidizer in ACN 4 x 2.5 L

Liquid Reagents (continued)


L260045-06 Oxidizer 0.02 M for ABI Instruments 6 x 450 ml

L320045-01 TCA Deblock for ABI Instruments 1 x 450 ml

L3300182-06 Activator 42 0.1 M 6 x 180 ml

L8300452-06 Activator 42 0.1 M 6 x 450 ml

L8300462-06 Activator 42 0.25 M 6 x 450 ml

L8300451-06 ETT Activator 0.25 M 6 x 450 ml

L340018-06 Cap A for ABI Instruments 6 x 180 ml


L350018-06 Cap B for ABI Instruments 6 x 180 ml





L370018-06 Fast Deprotection Cap A for ABI Instruments 6 x 180 ml

L370045-06 Fast Deprotection Cap A 6 x 450 ml

L380018-06 DCI Activator 0.25 M for ABI Instruments 6 x 180 ml

L880045-06 DCI Activator 0.25 M 6 x 450 ml

Compatible with Expedite and Polygen Instruments

L810045-06 Acetonitrile for 8900 Instruments 6 x 450 ml

L820090-06 TCA Deblock for 8900 Instruments 6 x 900 ml

L8300202-06 Activator 42 0.1 M 6 x 200 ml

L8300212-06 Activator 42 0.25 M 6 x 200 ml

L830045-06 Activator 42 0.1 M 6 x 450 ml

L8300462-06 Activator 42 0.25 M 6 x 450 ml

L840020-06 Cap A for 8900 Instruments 6 x 200 ml


L850020-06 Cap B for 8900 Instruments 6 x 200 ml


L860020-06 Oxidizer 0.02 M for 8900 Instruments 6 x 200 ml


L870020-06 Fast Deprotection Cap A for 8900 Instruments 6 x 200 ml


L880020-06 DCI Activator 0.25 M for 8900 Instruments 6 x 200 ml


Compatible with Äkta and Oligo Pilot Instruments

L520251-04 DCA Deblock (Toluene) 4 x 2.5 L

L540250-01 Cap A for Äkta and Oligo Pilot 1 x 2.5 L

L550250-01 Cap B1 for Äkta and Oligo Pilot 1 x 1.25 L


L560250-04 Oxidizer 0.05 M for Äkta and Oligo Pilot 4 x 2.5 L

52

Products Activator 42

Activator 42®

Activator 42 introduces unprecedented

activation power to phosphoramidite coupling

reactions. This novel activator provides unique

opportunities to speed up oligonucleotide

synthesis and to improve on product yield.

Key features of Activator 42

• The highest activation efficiency in the industrycompared to other activators

• Promotes ultrafast DNA couplings (coupling time less than 15 seconds)

• Promotes rapid RNA couplings (coupling time 6 minutes)

• Excellent solubility in acetonitrile (greater than 0.9 M)

• Not hygroscopic

• Safe to handle (no explosive properties)

• Very high overall yield in DNA and RNA synthesis

Solid phase oligonucleotide synthesis withphosphoramidites consists of a sequence of threeconsecutive reaction steps which are repeated in acyclical manner, deblocking, coupling and oxidation.

Whereas deblocking and oxidation reactionsproceed with nearly quantitative yields in state-of-the-art oligonucleotide synthesis, the couplingreactions, although high yielding, determine theoverall efficiency of the process. Coupling yields aredriven by a variety of factors, including amidite andsolid support quality, water content of the couplingmedium and the choice of activator moleculeemployed. An ideal activator should promote thecoupling of standard DNA amidites as well as thecoupling of more sterically demanding amidites(e.g. 2'O-TBDMS-RNA amidites) in a highly efficientmanner. The activator should have excellentsolubility in the coupling medium (i.e., acetonitrile)in order to avoid undesired precipitation orcrystallization, should not be hygroscopic, shouldbe safe to handle and should not lead to sidereactions in oligonucleotide synthesis. Thesedesired properties can be attributed to a newpowerful activator molecule which gives superiorperformance compared to the other commercialactivators such as 5-ethylthio-1H-tetrazole (ETT),5-benzylthio-1H-tetrazole (BTT) and4,5-dicyanoimidazole (DCI).

Activation efficiency for 2'O-TBDMS-RNA amiditesActivator 42 > ETT = BTT

Activation efficiency for standard DNA amiditesActivator 42 > DCI

Activator 42Catalog No. Description Unit

L0302502-04 Activator 42 0.1 M 4 x 2.5 L

L3300182-06 Activator 42 0.1 M 6 x 180 ml

L8300452-06 Activator 42 0.1 M 6 x 450 ml

L8300202-06 Activator 42 0.1 M 6 x 200 ml

L0302512-04 Activator 42 0.25 M 4 x 2.5 L

L8300462-06 Activator 42 0.25 M 6 x 450 ml

L8300212-06 Activator 42 0.25 M 6 x 200 ml

Other quantities and packaging are available upon request.

http://www.sigmaaldrich.com/content/safc-supply-solutions/en-us/home/oligo-raw-materials/our-offer/product-breadth/activator-42.html?cm_mmc=social-_-scribd-_-proligo%20reagents-_-pdf

53

Product List

DNA Pharmadites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

RNA Pharmadites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Standard DNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Fast Deprotection Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Fast Deprotection RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

2’0-Methyl RNA Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

DMT-2'Fluoro Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Labels and Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Non-Standard Nucleosides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Phosphate-ON Phosphoramidite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

NPPOC Phosphoramidites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

DNA CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Fast Deprotection CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Fast Deprotection RNA CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

2’0-Methyl RNA CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

DNA Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Fast Deprotection RNA Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

2’0-Methyl RNA Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Amino-ON CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Universal CPG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Liquid Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Activator 42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

54

Products Product List

DNA PharmaditesCatalog No. Description

A111P00-C DMT-dA(bz) Pharmadite

C111P00-C DMT-dC(bz) Pharmadite

G111P00-C DMT-dG(ib) Pharmadite

T111P00-C DMT-dT Pharmadite

RNA Pharmadites A211P00-C DMT-2'O-TBDMS-rA(bz) Pharmadite

C213P00-C DMT-2'O-TBDMS-rC(ac) Pharmadite

G211P00-C DMT-2'O-TBDMS-rG(ib) Pharmadite

U211P00-C DMT-2'O-TBDMS-rU Pharmadite

Standard DNA PhosphoramiditesCompatible with Expedite and Polygen Instruments























Standard DNA Phosphoramidites (cont.)Compatible with MerMade Instruments (8oz 28/400 bottle)































55

Fast Deprotection PhosphoramiditesCompatible with Expedite and Polygen Instruments


























Compatible with MerMade Instruments (8oz 28/400 bottle)
















RNA Phosphoramidites Compatible with Expedite and Polygen Instruments











A211061-01 DMT-2'O-TBDMS-rA(bz) Amidite 1 x 1 g

C213061-01 DMT-2'O-TBDMS-rC(ac) Amidite 1 x 1 g

G211061-01 DMT-2'O-TBDMS-rG(ib) Amidite 1 x 1 g


Fast Deprotection RNA PhosphoramiditesCompatible with Expedite and Polygen Instruments















Compatible with MerMade Instruments





Bulk Quantities





56


Labels and ModificationsCompatible with Expedite and Polygen Instruments


M010982-01 ssH-Linker 1 x 0.25 g

M010882-01 TFA Hexylaminolinker 1 x 0.25 g







M010932-01 ssH-Linker 1 x 0.25 g

M010832-01 TFA Hexylaminolinker Amidite 1 x 0.25 g






Non-Standard NucleosidesCompatible with Expedite and Polygen Instruments









Phosphate-ON PhosphoramiditeCompatible with Expedite and Polygen Instruments





NPPOC PhosphoramiditesCatalog No. Description Unit

A112N01-01 NPPOC-dA(tac) Amidite 1 x 1 g

C114N01-01 NPPOC-dC(ib) Amidite 1 x 1 g

G114N01-01 NPPOC-dG(ipac) Amidite 1 x 1 g

T111N01-01 NPPOC-dT Amidite 1 x 1 g

DMT-2'Fluoro PhosphoramiditesCatalog No. Description Unit

C213281-01 DMT-2'Fluoro-dC(ac) Amidite, 89 1 x 0.25 g

C213231-01 DMT-2'Fluoro-dC(ac) Amidite, ABI 1 x 0.25 g

C213233-01 DMT-2'Fluoro-dC(ac) Amidite, ABI 1 x 1 g

U211281-01 DMT-2'Fluoro-dU Amidite, 89 1 x 0.25 g

U211231-01 DMT-2'Fluoro-dU Amidite, ABI 1 x 0.25 g

U211233-01 DMT-2'Fluoro-dU Amidite, ABI 1 x 1 g

2’0-Methyl RNA PhosphoramiditesCatalog No. Description Unit

Compatible with Expedite Instruments


















C213161-01 DMT-2'O-Me-rC(ac) Amidite 1 x 1 g



Bulk Quantities


A212110-01 DMT-2'O-Me-rA(tac) Amidite 1 x 10 g



G212110-01 DMT-2'O-Me-rG(tac) Amidite 1 x 10 g


57

DNA CPGCatalog No. Description Unit




T301001-01 CPG 500Å dT 30-40 �mol/g 1 x 1 g




T301010-01 CPG 500Å dT 30-40 �mol/g 1 x 10 g




T401001-01 CPG 1000Å dT 25-35 �mol/g 1 x 1 g




T401010-01 CPG 1000Å dT 25-35 �mol/g 1 x 10 g

Fast Deprotection CPGCatalog No. Description Unit















Fast Deprotection RNA CPGCatalog No. Description Unit

A602001-01 CPG 500Å rA(tac), 25-35 �mol/g 1 x 1 g

C602001-01 CPG 500Å rC(tac), 25-35 �mol/g 1 x 1 g

G602001-01 CPG 500Å rG(tac), 25-35 �mol/g 1 x 1 g

U601001-01 CPG 500Å rU, 25-35 �mol/g 1 x 1 g

2’0-Methyl RNA CPGCatalog No. Description Unit

A601101-01 CPG 500Å 2'O-Methyl-rA(bz), 30-40 �mol/g 1 x 1 g

C602101-01 CPG 500Å 2'O-Methyl-rC(tac), 30-40 �mol/g 1 x 1 g

G601101-01 CPG 500Å 2'O-Methyl-rG(ib), 30-40 �mol/g 1 x 1 g

U601101-01 CPG 500Å 2'O-Methyl-rU, 30-40 �mol/g 1 x 1 g

58


Fast Deprotection RNA ColumnsCompatible with Expedite Instruments











2’0-Methyl RNA ColumnsCompatible with Expedite Instruments











DNA Columns (cont.)Compatible with ABI 3900 Instruments


A911010-01 Column Polystyrene 40 dA(bz), 40 nmol, ABI 3900

1 x 100

C911010-01 Column Polystyrene 40 dC(bz), 40 nmol, ABI 3900

1 x 100

G915010-01 Column Polystyrene 40 dG(dmf), 40 nmol, ABI 3900

1 x 100

T911010-01 Column Polystyrene 40 dT, 40 nmol, ABI 3900 1 x 100

A921010-01 Column Polystyrene 40 dA(bz), 0.2 µmol, ABI 3900

1 x 100

C921010-01 Column Polystyrene 40 dC(bz), 0.2 µmol, ABI 3900

1 x 100

G925010-01 Column Polystyrene 40 dG(dmf), 0.2 µmol, ABI 3900

1 x 100

T921010-01 Column Polystyrene 40 dT, 0.2 µmol, ABI 3900 1 x 100

DNA ColumnsCompatible with Expedite Instruments


A311010-01 Column CPG 500Å dA(bz), 50 nmol 1 x 100

C311010-01 Column CPG 500Å dC(bz), 50 nmol 1 x 100

G311010-01 Column CPG 500Å dG(ib), 50 nmol 1 x 100

T311010-01 Column CPG 500Å dT, 50 nmol 1 x 100

















Compatible with Expedite & ABI Instruments

A341010-01 Column CPG 500Å dA(bz), 50 nmol, ABI/89 1 x 100

C341010-01 Column CPG 500Å dC(bz), 50 nmol, ABI/89 1 x 100

G341010-01 Column CPG 500Å dG(ib), 50 nmol, ABI/89 1 x 100

T341010-01 Column CPG 500Å dT, 50 nmol, ABI/89 1 x 100








T361010-01 Column CPG 500Å dT, 1 �mol, ABI/89 1 x 100








T461010-01 Column CPG 1000Å dT 0.2 �mol, ABI/89 1 x 100

59

Liquid ReagentsCatalog No. Description Unit

L010010-06 Amidite Diluent (Acetonitrile) 6 x 100 ml

L010250-04 Acetonitrile 4 x 2.5 L






L020250-04 TCA Deblock 4 x 2.5 L

L0202502-04 TFA Deblock Toluene 4 x 2.5 L

L020251-04 DCA Deblock 4 x 2.5 L



L0302502-04 Activator 42 0.1 M 4 x 2.5 L

L0302512-04 Activator 42 0.25 M 4 x 2.5 L

L0302501-04 ETT Activator 0.25 M 4 x 2.5 L

L040250-01 Cap A 1 x 2.5 L

L040250-04 Cap A 4 x 2.5 L

L040251-01 Cap A for ABI Instruments 1 x 2.5 L

L040400-01 Cap A 1 x 4 L

L050250-01 Cap B 1 x 2.5 L

L050250-04 Cap B 4 x 2.5 L

L050251-01 Cap B for ABI Instruments 1 x 2.5 L

L050400-01 Cap B 1 x 4 L

L060250-04 Oxidizer 0.02 M 4 x 2.5 L

L060251-04 Oxidizer 0.1 M for ABI Instruments 4 x 2.5 L

L060252-04 Oxidizer 0.02 M for ABI 3900 Instruments 4 x 2.5 L

L060400-04 Oxidizer 0.02 M 4 x 4 L

L070250-01 Fast Deprotection Cap A 1 x 2.5 L

L070400-01 Fast Deprotection Cap A 1 x 4 L





ACN Based Liquid Reagents

LB40250-01 Cap A ACN 1 x 2.5 L

LB50250-01 Cap B ACN 1 x 2.5 L

LR40250-01 Cap 1 in ACN 1 x 2.5 L

LR50250-01 Fast Deprotection Cap 2 in ACN 1 x 2.5 L

LR60250-04 Oxidizer in ACN 4 x 2.5 L

Universal CPGCatalog No. Description Unit




M401010-01 Universal CPG 1000Å dT 25-35 � mol/g 1 x 10 g

Amino-ON CPGBulk CPG


M020101-01 Amino-ON CPG 500Å, 30-40 �mol/g 1 x 0.25 g

M020111-01 Amino-ON CPG 500Å, 30-40 �mol/g 1 x 1 g

Product List

60

Products

Liquid Reagents (continued)



L320045-01 TCA Deblock for ABI Instruments 1 x 450 ml

L3300182-06 Activator 42 0.1 M 6 x 180 ml

L8300452-06 Activator 42 0.1 M 6 x 450 ml

L8300462-06 Activator 42 0.25 M 6 x 450 ml

L8300451-06 ETT Activator 0.25 M 6 x 450 ml








L370018-06 Fast Deprotection Cap A for ABI Instruments 6 x 180 ml


L380018-06 DCI Activator 0.25 M for ABI Instruments 6 x 180 ml


Compatible with Expedite and Polygen Instruments

L810045-06 Acetonitrile for 8900 Instruments 6 x 450 ml

L820090-06 TCA Deblock for 8900 Instruments 6 x 900 ml

L8300202-06 Activator 42 0.1 M 6 x 200 ml

L8300212-06 Activator 42 0.25 M 6 x 200 ml

L830045-06 Activator 42 0.1 M 6 x 450 ml

L8300462-06 Activator 42 0.25 M 6 x 450 ml







L870020-06 Fast Deprotection Cap A for 8900 Instruments 6 x 200 ml


L880020-06 DCI Activator 0.25 M for 8900 Instruments 6 x 200 ml


Compatible with Äkta and Oligo Pilot Instruments

L520251-04 DCA Deblock (Toluene) 4 x 2.5 L

L540250-01 Cap A for Äkta and Oligo Pilot 1 x 2.5 L



L560250-04 Oxidizer 0.05 M for Äkta and Oligo Pilot 4 x 2.5 L

Activator 42Catalog No. Description Unit

L0302502-04 Activator 42 0.1 M 4 x 2.5 L

L3300182-06 Activator 42 0.1 M 6 x 180 ml

L8300452-06 Activator 42 0.1 M 6 x 450 ml

L8300202-06 Activator 42 0.1 M 6 x 200 ml

L0302512-04 Activator 42 0.25 M 4 x 2.5 L

L8300462-06 Activator 42 0.25 M 6 x 450 ml

L8300212-06 Activator 42 0.25 M 6 x 200 ml

Strength In Our HistoryOur beginnings are aligned with theinfancy of nucleic acid synthesistechnologies. In 1981, Professor HubertKöster founded Biosyntech GmbH,incorporating proprietary nucleic acidsynthesis technologies in Hamburg,Germany. Since that time, the entireindustry has undergone numeroustransformations, and our nucleic acidchemistry expertise and manufacturingcapabilities have remained at its forefront.

Today, Proligo® Reagents from SAFCSupply Solutions® are recognized theworld over for their quality. Our historyof providing DNA and RNA synthesisreagents and supporting services is onecustomers have depended upon in theiroglionucleotide programs for over 27 years.




SAFC Supply Solutions® recognizes that, as products move through pharmaceutical and diagnostic development, technologies and compliance requirements evolve.

With over 25 years of experience in our Hamburg manufacturing facility, we bring you Proligo® Reagents, a dedicated and comprehensive line of raw materials for oligonucleotides synthesis including DNA and RNA Pharmadites, standard and modified Amidites, Linkers & Modifiers, Supports & Solvents.

Contact your local representative to learn more about our technical and quality package.

To be inspiredmeet us at theyearly TIDESshow (US)

1981 Biosyntech GmbH proprietarynucleic acid synthesistechnologies founded byProfessor Hubert Köster

1986 Biosyntech acquired by Milligen,a division of Millipore®, Inc.

1991 Transfer of Biosearch chemicaloperations from California toHamburg, Germany

1993 First ISO 9001 biotechnologycompany certified in Germany

1994 Integration into PerSeptiveBiosytems®, Inc.

1995 Acquisition of Controlled PoreGlass (CPG®) technology

1996 Manufacturing facilitiesimproved to state-of-the-art

1998 PerSeptive Biosystems®, Inc.merges with Perkin-Elmer®

Corporation

1998 Proligo® Reagents founded bySKW and NeXstar

2002 Proligo® Reagents multi-tonmanufacturing capabilitiesintroduced

2005 Proligo® Reagents purchased bySigma-Aldrich, Inc. for its SAFC®

custom manufacturing group

To place an order or inquire aboutcustom manufacturing contact yourlocal SAFC representative or visitwww.safcsupplysolutions.com



Proligo® Reagents Nucleic acid solutions for genomic developmentPhosphoramidites / Modifiers / Supports / Liquid Reagents



SAFC International SitesGlobal E-mail: [email protected]

ArgentinaTel: +54 11 4556 1472Fax: +54 11 4552 1698E-Mail: [email protected]

AustraliaFree Tel: 1800 800 097 Free Fax: 1800 800 096Tel: +61 (0)2 9841 0555Fax: +61 (0)2 9841 0500E-Mail: [email protected]

AustriaTel: +43 (0)1 605 81 91 Fax: +43 (0)1 605 81 20E-Mail: [email protected]

BelgiumFree Tel: 0800 99560Free Fax: 0800 99561 Tel: +31 78 6205414Fax: +31 78 6205424E-Mail: [email protected]

BrazilTel: +55 11 3732 3100Fax: +55 11 3733 5151E-Mail: [email protected]

CanadaFree Tel: 1800 565 1400Free Fax: 1800 265 3858Tel: +1 905 829 9500Fax: +1 905 829 9292E-Mail: [email protected]

ChinaTel: +86 21 6386 2766Fax: +86 21 6386 3966E-Mail: [email protected]

Czech RepublicTel: +420 246 003 200Fax: +420 246 003 291E-Mail: [email protected]

DenmarkTel: +45 43 565 900 Fax: +45 43 565 905E-Mail: [email protected]

FinlandTel: +358 9 350 9250Fax: +358 9 350 92555E-Mail: [email protected]

FranceTel: +33 (0)4 74 82 2882Fax: +33 (0)4 74 82 2890E-Mail: [email protected]

GermanyTel: +49 (0)89 6513 1920Fax: +49 (0)89 6513 1919E-Mail: [email protected]

GreeceTel: +30 2 10 994 8010Fax: +30 2 10 994 3831E-Mail: [email protected]

HungaryTel: +36 (06) 1 235 9066 Fax: +36 (06) 1 235 9050Ingyenes zöldtelefon: 06 80 355 355Ingyenes zöld fax: 06 80 344 344E-Mail: [email protected]

IndiaBangaloreTel: +91 80 5112 7272Fax: +91 80 5112 7473New Delhi Tel: +91 11 2616 5477Fax: +91 11 2616 5611Mumbai Tel: +91 22 2570 2364Fax: +91 22 2579 7589Hyderabad Tel: +91 40 5531 5488Fax: +91 40 5531 5466E-Mail: [email protected]

IrelandTel: +353 (0)1 404 1903 Fax: +353 (0)1 404 1911E-Mail: [email protected]

IsraelFree Tel: +1 800 70 2222 Tel: +972 8 948 4100 Fax: +972 8 948 4200 E-Mail: [email protected]

ItalyTelefono: +39 02 3341 7350Fax: +39 02 3341 7201E-Mail: [email protected]

JapanTel: +81 (0)3 5796 7340Fax: +81 (0)3 5796 7345E-Mail: [email protected]

KoreaTel: +82 (0)31 329 9000Fax: +82 (0)31 329 9090E-Mail: [email protected]

MalaysiaTel: +60 3 5635 3321Fax: +60 3 5635 4116E-Mail: [email protected]

MexicoFree Tel: 01 800 007 5300Free Fax: 01 800 712 9920E-Mail: [email protected]

The NetherlandsTel: +31 (0)78 620 5414Fax: +31 (0)78 620 5424Free Tel: 0800 022 9092Free Fax: 0800 022 9093E-Mail: [email protected]

New ZealandFree Tel: 0800 936 666Free Fax: 0800 937 777

NorwayTel: +47 (0)23 176 000Fax: +47 (0)23 176 010E-Mail: [email protected]

PolandTel: +48 61 829 0100Fax: +48 61 829 0120E-Mail: [email protected]

PortugalTel: +351 21 924 25 55Fax: +351 21 924 26 10Free Tel: 800 20 21 80Free Fax: 800 20 21 78E-Mail: [email protected]

RussiaTel: +7 495 975 3321Fax: +7 495 975 4792E-Mail: [email protected]

SingaporeTel: +65 6779 1200Fax: +65 6779 1822E-Mail: [email protected]

South AfricaFree Tel: 0800 1100 75Free Fax: 0800 1100 79Tel: +27 11 979 1188Fax: +27 11 979 1119E-Mail: [email protected]

SpainTel: +34 91 657 2073 Fax: +34 91 490 5785 E-Mail: [email protected]

SwedenTel: +46 (0)8 742 4200 Fax: +46 (0)8 742 4243E-Mail: [email protected]

SwitzerlandSwiss Free Call: 0800 80 00 80Tel: +41 (0) 81 755 27 32Fax: +41 (0) 81 755 27 70E-Mail: [email protected]

United KingdomPooleTel: +44 (0)1202 712 305Fax: +44 (0)1202 712 235GillinghamTel: +44 (0)1202 712305Fax: +44 (0)1202 712235ManchesterTel: +44 (0)161 232 5500Fax: +44 (0)161 232 5501E-Mail: [email protected]

United StatesToll Free: 800 244 1173Call Collect: 314 534 4900Toll Free Fax: 800 368 4661Fax: 314 652 0000E-Mail: [email protected]

SAFC Proligo® ReagentsGeorg-Heyken Str.1421147 HamburgGermanyTel: +49 407 970 2250Fax: +49 407 970 2100E-Mail: [email protected]


KMI043530408

SAFC Supply Solutions®, Pharmadite®, SAFC Proligo® Reagents, andActivator 42® are a registered trademarks of Sigma-Aldrich

Biotechnology L.P. and Sigma-Aldrich Co.

Millipore® and CPG® are U.S. registered trademarks owned by MilliporeCorporation or an affiliated company.

Perkin-Elmer® and Perseptive Biosystems® are registered trademarks ofthe Perkin-Elmer Corporation, PerSeptive Biosystems, Inc. or other

subsidiaries in the U.S. and certain other countries.

ABI® is a registered trademark of Applera Corporation or its subsidiaries.

Expedite™ is a trademark of Applera Corporation or its subsidiaries.

PolyGen® is a registered trademark of PolyGen GmbH.

*LNA® / Locked Nucleic Acid® is a registered trademark of Exiqon A/S, Vedbaek, Denmark.

Cy trademarks are licensed through Molecular Probes which is now fully owned by Invitrogen.

All other trademarks are the property of their respective owners.Reproduction forbidden without permission.

LNA oligonucleotides and phosphoramidites are sold under license from Exiqon A/S for research use only. Not for resale or for therapeutic

use or use in humans. Specifications are subject to change.

© 2008 SAFC All rights reservedPrinted in USA



safc supply solutions - proligo® reagents catalog

Documents