1. DNA Enzyme reactions Ligation Restriction enzymes Helicase enzymes Polymerization Strand-displacing polymerases

2. Big Picture - Enzymes Exonucleases Endonucleases Restriction Endonucleases – Type I – cut elsewhere of recognition sites – Type II – cut within recognition sites http://www.eplantscience.com/index_files/biotechnology/Genes%20&%20Genetic%20Engineer ing/Tools%20of%20Genetic%20Engineering/biotech_enzymes.php

3. Ligation Self-assembled DNA Nanostructures and DNA Devices, Nanofabrication Handbook, Taylor and Francis 2012, with Nikhil Gopalkrishnan, Thom LaBean and John Reif http://www.bio.miami.edu/dana/pix/phosphodiester.jpg Ligase – “to bind” or “to glue together” T4 DNA Ligase – a single polypeptide, MW ~ 86,000 daltons, {pH 7.5 – 8.0, 10 mM Mg2+, DTT, NaCl 200 mM to stop reaction}

4. Restriction Enzymes Self-assembled DNA Nanostructures and DNA Devices, Nanofabrication Handbook, Taylor and Francis 2012, with Nikhil Gopalkrishnan, Thom LaBean and John Reif

5. Restriction Endonucleases Nicking Enzymes Restriction Enzymes

6. http://www.scq.ubc.ca/restriction-endonucleases-molecular-scissors-for-specifically-cutting-dna/

7. DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme www.cs.duke.edu/~reif/paper/peng/.../talk.WalkerDesign.ppt

8. DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme www.cs.duke.edu/~reif/paper/peng/.../talk.WalkerDesign.ppt http://www.angelfire.com/sc3/toxchick/molbiolab/molbiolab01.html

9. DNA 101: Enzyme Ligation, Restriction Sticky ends DNA ligase DNA restriction enzyme www.cs.duke.edu/~reif/paper/peng/.../talk.WalkerDesign.ppt http://www.angelfire.com/sc3/toxchick/molbiolab/molbiolab01.html

10. Helicase Enzymes Helicase enzymes are motor proteins that moving along a DNA double helix to denature its structure (unwind the double helix) independent of temperature. In particularly, helicase enzymes directionally break hydrogen bonds between base pairing in DNA double helix. http://click4biology.info/c4b/3/chem3.4.htm http://www.pdbj.org/eprots/index_en.cgi?PDB%3A3BEP

11. Polymerization Denaturation of target (template) – Usually 95 o C Annealing of primers – Temperature of annealing is dependent on the G+C content – May be high (no mismatch allowed) or low (allows some mismatch) stringency Extension (synthesis) of new strand Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

12. 5’ 3’ 5’ Target 1. Denature 2. Anneal primers 3. Extend primers Two copies of target 1. Denature 2. Anneal primers 3. Extend primers Four copies of target AMPLIFICATION BY PCR Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

13. PCR: First 4 Cycles Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

14. PCR: Completed Amplification Cycle Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

15. POLYMERASE CHAIN REACTION Primers (may be specific or random) Thermostable polymerase – Taq pol – Pfu pol – Vent pol Target nucleic acid (template) – Usually DNA – Can be RNA if an extra step is added Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

16. Features of Primers Types of primers – Random – Specific Primer length – Annealing temperature – Specificity Nucleotide composition Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

17. PCR Primers Primers are single-stranded 18–30 b DNA fragments complementary to sequences flanking the region to be amplified. Primers determine the specificity of the PCR reaction. The distance between the primer binding sites will determine the size of the PCR product. Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

18. TmTm For short (14–20 bp) oligomers: – T m = 4° (GC) + 2° (AT) Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

19. ASSUMPTIONS Product produced is product desired – There is always the possibility of mismatch and production of artifacts – However, if it is the right size, its probably the right product Product is from the orthologous locus – Multigene families and pseudogenes Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

20. Thermostable DNA Polymerase: Yellowstone National Park Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

21. Alvin Submersible for Exploration of Deep Sea Vents Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

22. Thermostable Polymerases Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

23. Performing PCR Assemble a reaction mix containing all components necessary for DNA synthesis. Subject the reaction mix to an amplification program. Analyze the product of the PCR reaction (the amplicon). Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

24. A Standard PCR Reaction Mix 0.25 mM each primer 0.2 mM each dATP, dCTP, dGTP, dTTP 50 mM KCl 10 mM Tris, pH 8.4 1.5 mM MgCl 2 2.5 units polymerase 10 2 - 10 5 copies of template 50 ml reaction volume Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

25. PCR Cycle: Temperatures Denaturation temperature – Reduce double stranded molecules to single stranded molecules – 90–96 o C, 20 seconds Annealing temperature – Controls specificity of hybridization – 40–68 o C, 20 seconds Extension temperature – Optimized for individual polymerases – 70–75 o C, 30 seconds Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

26. Combinations Of Cycle Temperatures Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

27. Thermostable Polymerases Taq: Thermus aquaticus (most commonly used) – Sequenase: T. aquaticus YT-1 – Restorase (Taq + repair enzyme) Tfl: T. flavus Tth: T. thermophilus HB-8 Tli: Thermococcus litoralis Carboysothermus hydrenoformans (RT-PCR) P. kodakaraensis (Thermococcus) (rapid synthesis) Pfu: Pyrococcus furiosus (fidelity) – Fused to DNA binding protein for processivity Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

28. Amplification Reaction Amplification takes place as the reaction mix is subjected to an amplification program. The amplification program consists of a series of 20–50 PCR cycles. Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

29. Automation of PCR PCR requires repeated temperature changes. The thermal cycler changes temperatures in a block or chamber holding the samples. Thermostable polymerases are used to withstand the repeated high denaturation temperatures. Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

30. Avoiding Misprimes Use proper annealing temperature. Design primers carefully. Adjust monovalent cation concentration. Use hot-start: prepare reaction mixes on ice, place in preheated cycler or use a sequestered enzyme that requires an initial heat activation. – Platinum Taq – AmpliTaq Gold – HotStarTaq Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

31. Primer Design http://biotools.umassmed.edu/bioapps/primer3_www.cg i http://biotools.umassmed.edu/bioapps/primer3_www.cg i http://arbl.cvmbs.colostate.edu/molkit/rtranslate/index. html http://arbl.cvmbs.colostate.edu/molkit/rtranslate/index. html Avoid inter-strand homologies Avoid intra-strand homologies T m of forward primer = T m of reverse primer G/C content of 20–80%; avoid longer than GGGG Product size (100–700 bp) Target specificity Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

32. Product Cleanup Gel elution – Removes all reaction components as well as misprimes and primer dimers Solid phase isolation of PCR product (e.g., spin columns) DNA precipitation Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

33. Contamination Control Any molecule of DNA containing the intended target sequence is a potential source of contamination. The most dangerous contaminant is PCR product from a previous reaction. Laboratories are designed to prevent exposure of pre-PCR reagents and materials to post-PCR contaminants. Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

34. Contamination of PCR Reactions Most common cause is carelessness and bad technique. Separate pre- and post-PCR facilities. Dedicated pipettes and reagents. Change gloves. Aerosol barrier pipette tips. Meticulous technique 10% bleach, acid baths, UV light Dilute extracted DNA. Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

35. Strand Displacement Polymerases Donna C. Sullivan, Division of Infectious Diseases, University of Mississippi

36. The Amplification Phase Step 1 The exponential amplification process begins with altered targets (single- stranded partial DNA strands with restricted enzyme recognition sites) from the target generation phase. Lisa Smith & Apollo Kacsinta, Cal State LA, Strand Displacement Amplification

37. Step 2 An amplification primer binds to each strand at its complimentary DNA sequence. Lisa Smith & Apollo Kacsinta, Cal State LA

38. Step 3 DNA polymerase uses the primer to identify a location to extend the primer from its 3' end, using the altered target as a template for adding individual nucleotides. Lisa Smith & Apollo Kacsinta, Cal State LA

39. Step 4 The extended primer forms a double- stranded DNA segment containing a complete restriction enzyme recognition site at each end. Lisa Smith & Apollo Kacsinta, Cal State LA

40. Step 5 The restriction enzyme binds to the double stranded DNA segment at its recognition site. Lisa Smith & Apollo Kacsinta, Cal State LA

41. Step 6 The restriction enzyme dissociates from the recognition site after having cleaved only one strand of the double- sided segment, forming a nick. Lisa Smith & Apollo Kacsinta, Cal State LA

42. Step 7 DNA polymerase recognizes the nick and extends the strand from the site, displacing the previously created strand. Lisa Smith & Apollo Kacsinta, Cal State LA

43. Step 8 The recognition site is repeatedly nicked and restored by the restriction enzyme and DNA polymerase with continuous displacement of DNA strands containing the target segment. Lisa Smith & Apollo Kacsinta, Cal State LA

44. Step 9 Each displaced strand is then available to anneal with amplification primers similar to the action in step 2. The process continues with repeated nicking, extension and displacement of new DNA strands, resulting in exponential amplification of the original DNA target. Lisa Smith & Apollo Kacsinta, Cal State LA

45. Strand Displacement Amplification Lisa Smith & Apollo Kacsinta, Cal State LA

46. Further Reading DNAzymes for sensing, nanobiotechnology and logic gate applications – Willner et. al. Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers – Liu et. al. DNAzymes: From Creation In Vitro to Application In Vivo – Li et. al. FRET Study of a Trifluorophore-Labeled DNAzyme – Lu et. al.