Dr. Chaim Wachtel June 4, 2015

1. Dr. Chaim Wachtel June 4, 2015 Introduction to Real-Time PCR

2. Summary of Last Week Microarrays HTS (High Throughput Sequencing) Sequence entire DNA/RNA content of sample No need for prior knowledge Artifacts- in general there is at least one amplification step Analysis time- depends- can take days or months • Hybridization to probes • Need previous information to plan probes • Limit to number of probes on one array • Cost per sample • Analysis time-days

3. Real-Time PCR • What is it? • How does it work • How do you properly perform an experiment • Analysis

4. The Nobel Prize in Chemistry 1993 was awarded "for contributions to the developments of methods within DNA-based chemistry" jointly with one half to Kary B. Mullis "for his invention of the polymerase chain reaction (PCR) method"and with one half to Michael Smith "for his fundamental contributions to the establishment of oligonucleotide-based, site-directed mutagenesis and its development for protein studies". Michael Smith

5. PCR – A simple idea Polymerase Chain Reaction: Kary Mullis (1983) In vitro method for enzymatically synthesizing DNA The reaction uses two oligonucleotide primers that hybridize to opposite strands and flank the target DNA sequence that is to be amplified A repetitive series of cycles gives exponential accumulation of a specific DNA fragment Template denaturation Primer annealing Extension of annealed primers by the polymerase The number of target DNA copies doubles every PCR cycle (20 cycles  220≈106 copies of target)

6. Principle of PCR

7. Real-Time and End Point End point Real time

8. Difference PCR vs real-time PCR? Fluorescence is measured every cycle (signal  amount of PCR product). Curves rise after a number of cycles thatis proportional to the initial amount of DNA template. Comparison with standard curve gives quantification.

9. MIQE: the minimum information for the publication of qPCR experiments. http://www.rdml.org/miqe.php

13. The mRNA of the Arabidopsis Gene FT Moves from Leaf to Shoot Apex and Induces Flowering Tao Huang, Henrik Böhlenius, Sven Eriksson, François Parcy, and Ove Nilsson Science 9 September 2005: 1694-1696. 2005: Signaling Breakthroughs of the Year

14. Retraction WE WISH TO RETRACT OUR RESEARCH ARTICLE “THE MRNA OF THE ARABIDOPSIS GENE FT MOVES from leaf to shoot apex and induces flowering” (1). After the first author (T.H.) left the UmeåPlant Science Centre for another position, analysis of his original data revealed several anomalies. It is apparent from these files that data from the real-time RT-PCR were analyzed incorrectly. Certain data points were removed, while other data points were given increased weight in the statistical analysis. When all the primary real-time RT-PCR data are subjected to correct statistical analysis, most of the reported significant differences between time points disappear. Because of this, we are retracting the paper in its entirety.

15. Real-Time Machines • How do they work • What can you do with one • Gene expression • SNP detection • DNA detection (quantify) • How do you use them • Experiment design • Everything you need to know and more about RNA and RT-PCR

16. spectrofluorometer fiberoptic PCR tube in thermocycler First real-time PCR, 1991 “Fifty Years of Molecular Diagnostics” Clin Chem. 2005 Mar;51(3):661-71 (C.Wittwer, ed.)

17. First commercial real-time PCR instruments ABI 7700 – laser/fiberoptic-based ABI 5700 – CCD camera-based Idaho Technology LightCycler – capillary tubes

18. RT-PCR machines at Bar Ilan 7900HT Fast Real-Time PCR System (Sol Efroni’s lab) AB StepOnePlus Fast Real-Time PCR System Qiagen’s Rotor-gene (Oren Levy’s lab) Thermo PikoReal (Bachelet Lab) Bio-Rad CFX-96

19. Rotor-gene

20. Probing alternatives Non-specific detection Dyes: SYBR Green I, BEBO, BOXTO, EvaGreen... Specific detection TaqMan probe Molecular Beacon Light-Up probe Hybridization probes Primer based detection Scorpion primers QZyme Lux primers

21. SYBR Green binds to dsDNA SYBR Green binds toDNA, particularly to double-stranded DNA, giving strongly enhanced fluorescence. SYBR Green is sequence-dependent!

22. The TaqMan Probe The TaqMan probe binds to ssDNA at a combined annealing and elongation step. It is degraded by the polymerase, which releases the dye from the quencher.

23. Strand Deplacement-PCR Detection of two (or more) different target sequences in the same reaction.

24. qPCR technical workflow DNA Extraction Data Analysis Sampling qPCR RNA Extraction DNase treatment Reverse Transcription

25. Nucleic acid isolation and purification

26. Overview Sampling Accessibility and lysis Commonly used techniques RNA considerations Quality control

27. Why sample preparation? Make target available Remove inhibitors Remove fluorescent contaminants Preserve target integrity Concentrate target

28. Path Disruption Isolation Purification RNA DNA Reverse Transcription Real-time PCR Genomic DNA mRNA Plasmid DNA Total RNA Fragment DNA Nuclear RNA Phage DNA

29. Accessibility Sample disruption and homogenization Mechanical Grinding, Sonication, Vortexing, Polytron Physical Freezing Enzymatic Proteinase K, Lysozyme, Collagenase Chemical Guanidinium isothiocyanate (GITC), Alkali treatment, CTAB

30. Lysis Complete or partial lysis? Chaotropic lysis buffers: SDS, GITC, LiCl, phenol, sarcosyl Gentle lysis buffers: NP-40, Triton X-100, Tween, DTT

31. Purification principles Characteristics of nucleic acids Long, unbranched, negatively charged polymers Examples: Differential solubility Precipitation Strong affinity to surface Factors: pH, [salt], hydrophobicity

32. Purification techniques Solution based- eg Tri reagent, CsCl gradient Precipitation- ethanol, needs salt, multiple factors can influence precipitation Membrane based- spin columns (Qiagen and the like) Magnetic bead based

33. Solution based isolation • Most methods use hazardous reagents • Phenol/Chloroform extraction • Proteins, lipids, polysaccharides go into the organic phase or in the interphase. • DNA/RNA remains in aqueous phase • Caesium chloride density gradient ultracentrifugation • Time consuming • Ethidium Bromide (Lots and lots) • Acid guanidine phenol chloroform extraction • Commonly called TRIzol

34. Precipitation purification • Nucleic acids precipitate in alcohols • Salt (NaCl, NaAc) facilitates the process • Important factors: Temperature, time, pH, and amount

35. Membrane based isolation • Anion exchange technology • Spin column / silica gel membrane • Chaotropic salts (e.g. NaI or guanidine hydrochloride) bind H2O molecules • Loss of water from DNA changes shape and charge • DNA binds reversibly to silica membrane

36. Purification – GITC vs. column Organic liquids Pro: Higher yield Can handle larger amounts of cells Better for troublesome tissues (fatty tissue, bone etc) Con: Higher DNA contamination (for RNA isolation) Separate DNase I digestion with additional purification Spin columns Pro: Less contaminating DNA (for RNA isolation) On column DNase digestion Less loss of RNA Higher quality Easy to use Con: Limited loading capacity More expensive (?)

37. RNA Considerations RNA is chemically and biologically less stable than DNA Extrinsic and intrinsic ribonucleases (RNases) Specific and Nonspecific inhibitors

38. Stabilizing conditions Work on ice Process immediately Flash freeze sample in liquid nitrogen and store at -70°C until later use Store samples in stabilization buffer

39. Storage of nucleic acids Nuclease-free plasticware Eluted in nuclease-free water, TE or sodium citrate solution RNA: Neutral pH to avoid degradation Aliquot sample to avoid multiple freeze-thaw cycles Isolated RNA should be stored at -20 deg C or -70 deg C for even better protection in ethanol and not water.

40. Quality Control Spectroscopic methods Concentration, [NA] = A260 x e mg/ml Purity: A260 / A280 (≈1.8 for DNA, 2.0 for RNA) Dyes Quantification by fluorescence of DNA/RNA-binding dyes (Qubit) Electrophoresis (28S and 18S bands)

41. What is the BioAnalizer? • Microfluidic separations technology • RNA - DNA - Protein • 1µl of RNA sample (100 pg to 500 ng) • 12 samples analyzed in 30 min • Integrated analysis software: • Quantitation • Integrity of RNA

42. Bioanalyzer

46. Good RNA Quality Bad RNA Quality 10 RNA Quality Indicator 1 RNA Integrity: RQI

47. Publications on RNA integrity

48. DNase I treatment of RNA samples RT, No DNase No RT, No DNase RT, DNase No RT, DNase

49. qPCR technical workflow DNA Extraction Data Analysis Sampling qPCR RNA Extraction DNase treatment Reverse Transcription

50. Reverse transcription RT