Scanning Tunneling Microscopy of DNA Scanning Tunneling Microscopy of DNA molecules. molecules.

DNA Nanoelectronics: sequencing and DNA Nanoelectronics: sequencing and Imaging of single moleculesImaging of single molecules

Dzmitry YarotskiDzmitry YarotskiS. Kilina, S. Tretiak, A. Taylor, AV Balatsky(Center for Intergrated Nanotechnology, Los Alamos)

A. Talin(CINT, SANDIA)

CINT is one of five Department of Energy Nanoscience Centers.Centers.

Center for Nanophase Materials Sciences

Center for Functional Nanomaterials

Center for Integrated Nanotechnologies

Center for Nanoscale MaterialsMolecular Foundry

http://cint.lanl.gov; http://cint.sandia.gov

LANL Gateway Facility, LANL Gateway Facility, opened Aug 2006opened Aug 2006

3D Active Stereo Scientific VisualizationWe have developed visualization capabilities for simulation, theory and experiment for users. Our focu areas are:

Scanning Tunneling Microscopy and Spectroscopy of high temperature cuprates, heavy fermions and DNA

Heterogeneous structures of foams, poly-xtal, poly-meric and HE materials

Molecular Dynamics simulationsof phase transitions

3D active stereo demo of a large molecule in the graphics room at CINT.

Fakespace rear projection system with a 6’x8’ soft screen (behind screen sits a Christie Digital Mirage S+4K stereo projector with 3-chip DLP technology that delivers 5000 lumens (1 kW lamp) and SXGA+ 1400x1050 resolution).

Data by Kawai group

Raw data Same data using viz software

Potential for STM tunneling as an alternative sequencing and imagingtechnique. Fingerprints of molecules.

STM tunneling through DNA on a metallic substrate.

Historical review, Scanning Tunneling Spectrroscopy, Inelastic Tunneling

DNA nanoelectronics

Nanotechnology: Science and Engineering ofthe 21st Century

Size of structureExamples of Size

Year

NA

NO

MIC

RO

MA

CR

O

Top down

Syste

m Creatio

n

Bottom up

0.1 m

1 cm

1 mm

0.1 mm

10 μm

1 μm

0.1 μm

10 nm

1 nm

0.1 nm1940 1960 1980 2000 2020 2040

Tools, Pens, ---

Wire, Screws,

Fibre GlassOptics, MicroprobesThick Film, Microsensors

Hair, Skin

Bacteria, CD-bits64Mb-256Mb-ChipThickness of Gold foil,G bit-Chip

ProteinNanoparticels, widthOf DNAMolecule/FullerenesAtom Size

Utilization ofBiological principles

Physical lawsAnd

Chemical properties

Boundaries between nano/micro domains

(Still) Looking for a few new sequencing technologiesNanopore Sequencing

(Sequence-specific detection of single molecules)

Our casePossible?

Nature Biotech. Vercoutere et al. 2001

STM Tip

D.Branton et al. 2001

Tipsample

LDOSDOS

ε

eV

z

It

Scanning tunneling microscopy/spectroscopy

It ∝∫LDOSsample (ε) dεεF

εF + eV

∝

LDOSsample (ε)dIt dV

Spectroscopic map (LDOS map) can be obtained.

High Resolution STM Imaging of Single Molecular DNA

STM Tip

AG

T

A

CPS

PS

P PS S

S SS

SS

SS

S

SS

S

P

PP

PP P

P PP

P

SS

S

SS

SP

P

PPP

SS

SP

PP

PP

S SS

S

SS

PP

PS

C

GC

CG

A

A GC

CG T

T

GC

TA

G

GGC

CS S S

3.4nm

Surface

3.4nm

2nm

Fragile and large Bio-molecules!

• Pros and cons for single molecule sequencing•Is it competitive?•Bottleneck: sample preparation- slow – hour to 30 min•Once the STM starts scanning, takes ~ 1-100 microsec•This is not a live culture. True. •But a lot of conventionalapproaches do cut and destroy assayed material. All we are looking is a table : ATGC…• Clear alternative to the optical detection schemes dominating landscape of sequecing now.

STM: DNA on graphiteHighest resolution images of the timeHighest resolution images of the time

R.J. Driscoll et al., Nature 346, 294 (1990) P.G. Arscott et al., Nature 339, 484 (1989) G. Lee et al., Science 244, 475 (1989)

Steps on the graphite surface crossing domain boundary mimic DNASteps on the graphite surface crossing domain boundary mimic DNA molecule, rendering molecule, rendering HOPG unsuitable as reliable substrate for biomolecule depositionHOPG unsuitable as reliable substrate for biomolecule deposition

C.R. Clemmer et al., Science 251, 640 (1991)

W.M. Heckl et al, Ultramicroscopy 42-44, 1073 (1992)

Motivation for DNA nanoelectronics

Recently developed pulse injection method opens new perspectivesRecently developed pulse injection method opens new perspectives for STM studies of for STM studies of broad range of biological objects, especially of DNA molecule broad range of biological objects, especially of DNA molecule

• Single nstructure of individual nucleotide?

• Nucleotides has been differentiated by their size thus far. Need for further investigations of electronic response of various nucleotides.

• STM tunneling spectroscopy may become a new sequencing technique applicable to short single DNA molecules if theoretical predictions of difference in frequencies of vibrational modes of A-T and G-C bond are confirmed ucleotides has been imaged in the unfolded DNA. Is it possible to resolve the experimentally.

Ever decreasing size of electronic devices calls for fabricationEver decreasing size of electronic devices calls for fabrication approaches inspired by approaches inspired by biobio--selfself--assembly. STM may prove to be the tool for characterization of sassembly. STM may prove to be the tool for characterization of such structures.uch structures.

• In particular, optimization of the process of metallization of DNA-based wires can be achieved by exploration of the relation between geometrical arrangement of nanoparticles and electronic properties of the wire.

Pulse injection method

H. Tanaka and T. Kawai, JVST B15(3) 602-604 1997

Pulse valve opens for short period of time and injects DNA Pulse valve opens for short period of time and injects DNA solution into the vacuum chamber. During such solution into the vacuum chamber. During such ““freezefreeze--drydry”” procedure water evaporates faster than DNA aggregates, thus procedure water evaporates faster than DNA aggregates, thus

leaving a single DNA molecule on the substrateleaving a single DNA molecule on the substrate

Pulse injection method

Hiroyuki Tanaka et al, Surface Science, 432 (1999) L611-L616. Hiroyuki Tanaka et al, Surface Science 539, L531 (2003).

Show viz for these data

Experiments at Los Alamos

• New STM • DNA- Carbon Nanotube Hybrid

structures: preliminary results

WORKING!!Upgraded experimental setup

D. YarotskiLANL

DNADNA--Carbon Nanotube composite:Sample PreparationCarbon Nanotube composite:Sample Preparation

Surfactant‐based 

nanotube 

suspensions 

were 

prepared 

by 

sonicating 

purified 

SWCNT 

powder 

obtained 

from 

SES 

Research 

in 

1% 

by 

weight 

of 

Triton 

X‐100 

in 

water 

for 

several 

hours. The final concentration of SWCNTs in Triton X‐100 suspensions was ,0.1 mg/ ml.To 

form 

DNA‐based 

nanotube 

suspensions, 

a 

20‐mer 

DNA 

sequence 

of 

5’NH2

(C‐

6)GAGAAGAGAGCAGAAGGAGA‐3’ was 

prepared 

to 

approximately 

5 

mg/ml 

in 

phosphate 

buffer 

solution 

with 

pH 

7.4 

(PBS 

7.4). 

One 

mg 

of 

SWCNT 

was 

brought 

to 

approximately 

250 

microliters with the DNA solution, and then diluted to approximately 0.75 ml with PBS 7.4.The resulting mixture was sonicated at 0 °C for at least 90 min, and then centrifuged at 14 

000 rpm for 90 min.Small drop of the resulting solution has been deposited onto p‐doped Si(110) substrate and 

let dry. A.A. Talin et al., J. Vac. Sci. Technol. B 22(6), Nov/Dec 2004

Sample 

was 

heated 

to 

550oC for 30 min. 

Sample 

was 

heated 

to 

550oC for 60 min.

Sample 

was 

heated 

to 

300oC for 40 min.

Surface structure is very sensitive to the annealing temperature

and duration 

1.6 1.8 2.0 2.2 2.4 2.6 2.80

2

4

6

8

Cou

nt

Period Across CNT (nm)

2.5 3.0 3.5 4.0 4.5 5.0 5.50

2

4

6

8

Cou

nt

Period along CNT (nm)

AA

BB

DNA‐CNT: Periods of the structure along and across the CNT direction

Angle between A and B = 63.4o

Imaging conditions:Ub

=3 V; It

=10 pA; T=50 K

Peak at this position is also present when there is 

no obvious periodic modulation along CNT exists. It 

is due to shape of the structure itslef? 

Sample 

was 

heated 

to 

550oC 

for 

30 

min. 

before 

imaging 

to 

remove 

organic 

residue 

from 

the 

surface

Current prospectsCurrent prospects

Deposit the DNADeposit the DNA--CNT solution onto Au(111) or HOPG surface to CNT solution onto Au(111) or HOPG surface to eliminate heating in sample preparation and improve spatial resoeliminate heating in sample preparation and improve spatial resolutionlution

Acquire spatially resolved dI/dV spectroscopy on new samples ofAcquire spatially resolved dI/dV spectroscopy on new samples of the the DNADNA--CNT hybrids and look for correlation with structural informationCNT hybrids and look for correlation with structural information

Compare the results to the bare CNT samplesCompare the results to the bare CNT samples

Calculate hybrid structural and electronic properties (TCalculate hybrid structural and electronic properties (T--11 team) and 11 team) and compare to experimentcompare to experiment

Theory and modeling

• Realistic ab initio calculations• Comparison with the data• Future directions

Molecular Orbitals of C and C-derivatives

(HOMO)

Cytidine (LUMO)

Cytiside (LUMO)

(HOMO)

Eg=2.44 (2.49) eVEg=2.99eVEg=5.08eV

Eg=4.98 eVEg=5.56 eVEg=7.59 eV

Cytosine (LUMO)

(HOMO)

Eg=5.11 (5.28) eVEg=5.54 eVEg=7.57eV

B3LYPPBE1PBE

BHandHLYPEg=9.49 eV Eg=11.94 eVEg=11.8 eVHF

Eg=3.62 eV (3.56)PW91

DOS of DNA-bases

- 1 5

- 1 2

- 9

- 6

- 3

0

3

6

9T h y m in e

Ene

rgy,

eV

A d e n in e C y to s in e G u a n in e

Eg=5.28(4.47)

Eg=5.54 (4.86)

Eg=5.59(5.03)

Eg=5.41(4.45)(TDDFT)

Experimental Eg: 4.51-4.63 4.4-4.7 4.31-4.59 4.44-4.8

B3LYP

Electronic fingerprint of Guanine

• Electronic detection of a single Guanine• Work on other bases• Potential to image proteins.

0

0 . 2

0 . 4

0 . 6

0 . 8

1

- 3 - 2 - 1 0 1 2

0 4 8 2 0 5 0 _ 1 6 C h 4 . c s v0 4 8 2 0 5 0 _ 1 4 C h 4 . c s v

dI/dV / nS

V s / V

Top: 

Tanaka 

data on GuaninBottom

: 

Theory 

calculat

ionOn 

LDOS 

of G on 

Cu(111

)

Backed out full sequence for the observed chunk

aaaacgcgctacagtctgacgxxxxxgxgxxxxxgxxxgxxg

---xxxxxgxgxxxxxgxxxgxxg-- -----

aaaacgcgctacagtctgacg------

This shows that one can back out the dI/dV

features

on other bases in the sameMolecule.

Step A : identify portion you tunnel ing in g‐specific map

Step B: identify other bases in the same chunk.

DNA nanoelectronics and STM

• Community building and growing• Biology vs Physics: view as physical system• Very exciting possibilities at the interface of

Bio and Nano.• Be aware about standard: doped Si. This is a

very tough comparison. Reproducibility, lack of understanding. Nowhere near sequence reliability of PCR. Obvious strength: single molecule.

• Future is bright and full of challenges.