1. Thermus AQuaticus DNA polymerase SEQUENCE: MRGMLPLFEPKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTPED FPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGDESDNLPG VKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKLSWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPW PPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWT EEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAI GKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLCCCDPNLQNIPVRTPLGQRIRRGFIAEEGWLLVAL DYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLE EGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGV YPLAVPLEVEVGIGEDWLSAKE by Dave Phillis Spring 2010

2. Dna Replication

3. PCR Reaction

4. Helices and Beta Barrels and side chains

5. DNA and “O” helix

6. Magnesium metal

7. Magnesium Interactions

8. ALL ZINC

13. Hydrogen Bonding CTP

14. HYDROPHOBIC INTERACTIONS

15. ALL HYDRO AND H-BOND

16. ALL CTP

17. Sequence Alignment

19. Literature Cited 1., F.; Stoffel, S.; Saiki, R.; Myambo, K.; Drummond, R.; Gelfand, D., (1989) Isolation, Characterization, and Expression in Escherichia coli of the DNA Polymerase Gene from Thermus aquaticus. Journal of Biological Chemistry. 264:6427-6437. 2. Patel, P.; Kawate, H.; Adman, E.; Loeb, L., (2000) A single highly mutable catalytic site amino acid is critical for DNA polymerase fidelity. Journal of Biological Chemistry. Nov 7. 3. Steitz, T. (1999) DNA Polymerases: Structural Diversity and common Mechanisms. Journal of Biological Chemistry. 274: 17395-17398. 4. Urs, U.; Ramachandran, M.; Krishna Murthy, H., (1999) Structure of Taq polymerase shows a new orientation for the structure-specific nuclease domain. Acta Cryst. D55:1971-1977. 5. Villbrant, B. ; Sobek, H. ; Frey, B.; Schomburg, D., (2000) Domain exchange: chimeras of thermus aquaticus DNA polymerase, escherichia DNA polymerase I and thermotoga neapolitana DNA polymerase. Protein Engineering. 9:645-54. 6. Kim, Y.; Eom, S.; Wang, J.; Lee, D.; Suh, S.; Steitz, T., (1995) Crystal structure of Thermus aquaticus DNA polymerase Nature 376, 612-616 (17 August 1995) 7. Chien A, Edgar DB, Trela JM (1976). "Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus". J. Bact. 127 (3): 1550–7. 8. Saiki, RK; et al. (1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.". Science 239 (4839): 487–91. 9. Saiki, RK; et al. (1985). "Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia" Science 230 (4732): 1350–4 10. Lawyer FC, et al. (1993). "High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase...". PCR Methods Appl. 2 (4): 275–87. 11. Tindall KR and Kunkel TA (1988). "Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase". Biochemistry 27 (16): 6008–13