techniques and strategies in molecular medicine
TRANSCRIPT
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Techniques and strategies in molecular medicine
RNA detection and quantitation
Dr Shane DugganInstitute of Molecular Medicine
St James HospitalTCD
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Central Dogma
Cytokine
Receptor
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Why and how RNA• mRNA or transcript levels are immensely informative of
the state of a cell.• In general increases in the levels of a particular protein is
reflected by increases in the corresponding mRNA transcript.
• Changes in gene expression is important in the cellular response to external stimuli and to basic cellular function.
• Completion of human genome sequencing projects has displayed detailed regions of hypothetical genes, EST and the location of many known genes.
• Far more proteins than genes, splice variation.• Antibody production is laborious.• RNA based molecular techniques can exploit data from
the genome projects successfully.
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Introduction to RNA• Ribonucleic acid (RNA), a nucleic acid polymer
consisting of many nucleotides• Each nucleotide is made up of nitrogenous base, a
ribose sugar and a phosphate.• DNA deoxyribonucleic acid, ribose lacks one oxygen
atom by comparison to RNA. • RNA is usually single stranded as opposed to DNA
double stranded.• RNA utilises the nucleotide Uracil in place of thymine
found in DCA• 3 main types:-
– Messenger RNA (mRNA)– Ribosomal RNA (rRNA)– Transfer RNA (tRNA)
DNA Adenine-ThymineA—T
RNA Adenine-UracilA—U
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RNA extraction and purification strategies
• Tissue storage• Tissue disruption
• RNA storage
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RNA extraction and purification strategies
• Firstly DNA and RNA must be extracted from the cell or tissue of interest by:-
» Cell breakage (Lysis)» Removal of protein or DNA or RNA» Concentration of either DNA or RNA» Determination of purity and quantity
• In modern labs nucleic acids may be purified using silica membranes and spin column centrifugation (High salt).
• Contaminating DNA and RNA can be removed by treating the membranes with appropriate DNAses or RNAses.
• Nucleic acid quantitation may be determined by UV spectrophotometry with absorption at 260 nm.
• Contaminating protein- 260:280 ratio.
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RNA isolation
• Determinants of Cell lysis approach:-– Tissue type, Bone, connective, fatty tissues, Blood,
urine, plant, Bacterial.– Viral, cellular RNA– Storage in RNAlater/ICE preservative– Storage in liquid nitrogen– Quantity and quality of RNA required for downstream
applications– Cell lines generally not a problem
• Optimisation study definitely required.
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Tissue disruption
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Add Choloform
Mix and rest 5 mins
Centrifuge 15 mins
Homogenisation
Pre-chilledTri-reagent
Organic phase-Protein
Carefully remove Aqueous phase
Mix aqueous Phase with isopropanol
SpinPelletRNA
Re-suspendIn TE or H20
Aqueous phase-RNA
DNA precipitate
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Spin column purification•Great for cell lines•Cleaning up after Tri-reagent•Silica gel binding of RNA•Ethanol salt washes•Elute high quality RNa in H20•General Nucliec acid•Specific small RNA binding•On column DNA digestRneasy MinElute Cleanup•Ideal following Tri-reagent•Concentrates RNA •Fast, High-throughput
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Poly(A)+ RNA isolation•Utilizes polydT coated magnetic beads•Binds to poly A tail of mRNA•Avoids DNA, protein, rRNA and tRNA•Enriches transcripts by 30 fold•Less prone to DNA contamination
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RNA Quantitation• UV spectroscopy
– Consistant– Reliable– Easy– 260/280 ratio– 260/230 ratio
• Ribo green assay– RNA Standard curve– Accurate
• NanoDropFlourospectrometer
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RNA qualitation
• MOPS gel eletrophoesis– Stain with ethdium
bromide– Displaying ribosomal RNA
units.– mRNA too dilute to see,
but usually a smear when selected
– rRNA ration good indicator of a healthy sample
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RNA Qualitation• If samples of poor quality are used then suspect data will be generated, low
chip performance, high false discovery rate, missing biological variation
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Optimise RNA extraction protocol!
• Tissue or cell line• Cell sorted (FACS, macs beads etc)• Bio-bank or not• Preservative (RNAlater) or liquid nitrogen• Quantity and quality of RNA required for
downstream application• DNAse treatment required or correct
primer design.
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Polysomal RNA extraction!
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Northern/Southern blotting• Southern blotting is the name given to a
technique, originally described by Southern et al, for the transfer of DNA from a gel to a filter.
• Blotting usually refers to the transfer of any molecules from an electrophoresis gel to a solid membrane support.
• DNA or RNA that has been separated and held in this manner can by probed by hybridisation of complementary sequences.
• This complementary sequences are usually radio-labelled by in-vitro transcription of radio-labelled nucleotides (dNTP) usually dCTP.
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Northern blotting steps
• RNA isolation• Probe generation• Denaturing agarose gel electrophoresis• Transfer to solid support and immobilization• Pre-hybridisation and hybridisation with probe• Washing• Detection• Stripping and reprobing
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Synthesis of radio-labelled probe
• Radioactively labelled• Non-isotopically labelled (Biotin)• 3 main methodologies
– Random-priming of DNA probe– Asymmetric PCR probe generation– In vitro transcription of RNA
• Random priming is most traditional technique, best for radioactive probes.
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Gene sequence• In order to generate probes sequence information must
be available.• Blast, homology searching for region of gene with
greatest specificity.• Coding region, intron-exon boundary.• Probe length may vary but should be long enough to be
specific and short enough for optimal hybridisation.• Polymerase chain reaction (PCR) from DNA to generate
probe template.• PCR product is then labelled by priming with random
hexamers and random incorporation of radio-labelled dCTP.
• Remove unincorporated radio dCTP with spin columns
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Synthesis of radio-labelled probe
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Blotting / Hybridisation
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Dot Blot
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RNAse protection assay
• Northern in a tube• Probes generated as before• Increased sensitivity• Hybridisation occurs in solution where
target availability is maximal• Multiple target/probe acqusition/utilisation
is possible, determined by probe length.
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RNAse protection assay
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RT-PCR• Reverse transcription polymerase chain reaction (RT-
PCR)• A specific sequence is repeatedly amplified to generate
enough copies of the transcript to be visualised by ethidium bromide staining.
• RNA samples are transcribed into cDNA by a reverse transcriptase and then amplified by DNA polymerase as in PCR for northern probe generation.
• Powerful for rare transcripts and more sensitive than northern blotting and RPA analysis.
• Can be both relative quantification and absolute quantification (competitive RT-PCR)
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RT-PCR• Reverse transcription is a process utilised by
RNA viruses in the process of replication.• Reterotransposons• Reverse transcription is performed at 42ºC using
a reverse transcriptase such as M-MLV (Moloney murine leukemia virus)
• An oligo dT primer is utilised to prime the reaction
• It can be performed with minute quantities of RNA.
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RT-PCR
• Following the generation of a cDNA template the gene of interest is amplified in a cyclical manner by DNA polymerase:-– Denaturation (94ºC) Double stranded DNA is made
single stranded.– Annealing (Determined by primers 54ºC) Primers bind
to complementary DNA sequences– Extension (72ºC) DNA pol. can now transcribe new
complementary stretches of DNA starting at the site of primer annealing, incorporates nucleotides in a 5’to3’direction reading the sequence in a 3’to5’ manner.
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Cycle Copies1 2
2 4
4 16
10 1,024
15 32,768
20 1,048,576
25 33,554,432
30 1,073,741,824
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Primer design• Complementary to sequence of interest! Blast
searching to improve specificity.• Length between 18-24 bps is optimal• Share similar melting temperatures (Tm)• Primer pair most not share complementarities at
3’ ends, primer dimer• No palindromic sequences, hairpin loops.• G/C content 45-50%• Distance between primers, variable (150-500)• Intron-exon boundaries!!!
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RT-PCR optimisation• Most of the component of a PCR reaction may
be optimised to obtain maximum specificity and sensitivity:– Mg++ concentration– Template DNA concentration– Taq DNA polymerase used (proof reading
exonuclease)– dNTPs concentration (high may inhibit)– Primer to template ratio– Thermal cycling (1000bp/min extension, increase
denaturation if high GC content in primer)• Controls:- no template, no primer.
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PCR optimisation
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Cycle limitation The Result
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Competitive RT-PCR?
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Real-time RT-PCR• Dramatic increase in sensitivity achieved!• Fluorescent based version of RT-PCR• Increases in PCR product is directly proportional to a
fluorescent reporter.• This reporter may be viewed in a live mode thus giving
rise to real-time.• A profile of the PCR is then generated charting the
progress through the exponential phase to the plateau phase.
• A point in the linear phase may be chosen to examine gene expression differences between samples.
• The earlier this line is reached the more copies of that particular transcript was present.
• These movements are normalised by reference to a control house keeping gene if one is available.
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The concept
Reference gene
Gene of interest
Ct
∆Ct
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Examples
• FRET (Fluorescence resonance energy transfer) BASED:-– Taqman (Applied biosystems)– Molecular Beacons (Invitrogen)– Scorpions
• Sybr green– Emits signal upon binding to double stranded
DNA and excitation.– Not sequence specific
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5’-3’exonuclease activity
Numerous dyes availableReporter•FAM, VIC, TET, JOE, HEXQuencher•TAMRAReference dye•ROX, internal signal standard
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Genes of interest
Efficiencies 100%All function with identical PCR cycling conditions
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VIP• Prior to performing real time RT-PCR expts it is
important to determine an appropriate control housekeeping gene.
• Hypothesis, no such thing as a housekeeping gene????!
• Test a panel of non-changing genes GAPDH, Actin. 18srRNA etc
• Chose the gene with minimal variation across your samples when equal amounts of starting material has been used.
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PCR profile
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Linear scale
Log scale
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Primer optimisation Std/Dil curve
slope = -3.35Efficiency:- 99%Correlation coef:- 0.999
slope = -4.27Efficiency:-66%Correlation coef:- 0.985
E = (10-1/slope)-1 to calculate efficiency (E),
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Interpretation of results
• Standard curve method (Similar to primer optimisation)
• PFAFFL method (incorporates efficiencies)
• ∆∆Ct method• Determine the amount of accuracy/power
required to answer biological question.
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Standard CurveStd Curve•Relative
•Plasmid standard•cDNA dilution curve
•Quantitative•RNA standard•Copy number possible
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Comparative Ct of ∆∆Ct method
• For the ∆∆Ct calculation to be valid, the amplification efficiencies of the target and the endogenous reference must be approximately equal.
• ∆Ct= ∆Cttarget gene- ∆Ctcontrol geneis determined for each sample
• Average ∆Ct determined for calibrator (untreated sample)
• ∆∆Ct= ∆Ctsample- ∆Ctcalibrator is change in Ct• Relative fold change= 2(- ∆∆Ct)
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Example ∆∆Ct methodResting Treated17.67503 17.875984
GAPDH 17.79494 17.86698517.90083 17.892178
AVG 17.79027 17.87838233
22.6176 17.93654EGR1 22.29687 18.21179
22.06322 18.041883
-4.827333 -0.058157667-4.506605 -0.333407667-4.272958 -0.163500667
CAL Avg -4.535632
0.291701 -4.477474-0.029027 -4.202224-0.262674 -4.372131
1.224083 22.276860170.980081 18.407528120.833542 20.70821074
Rel FC 1.012568 20.46419967StDEV 0.197287 1.94617283
pvalue 6.66796E-05
0
5
10
15
20
25
Resting Treated
Series1
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Assay miniaturisation and automation
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Thanks for your attention.