Techniques used to study the DNA polymerase reaction pathway

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1804, Issue 5, 2010, Pages 1032-1040

  Joyce, Catherine M ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

DNA polymerase; Fluorescence; Kinetics; Reaction pathway

Indexed keywords

2 AMINOPURINE; DEUTERIUM; DNA POLYMERASE; RNA; SOLVENT; SULFUR;

DNA BINDING; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; PRIORITY JOURNAL; PROTON TRANSPORT; REVIEW; STEADY STATE;

ANIMALS; BIOLOGICAL ASSAY; DNA; DNA-DIRECTED DNA POLYMERASE; HUMANS; SUBSTRATE SPECIFICITY;

EID: 77949571174     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.07.021     Document Type: Review

References (44)

1. Johnson K.A., et al. Transient-state kinetic analysis of enzyme reaction pathways. In: Boyer P.D. (Ed). The Enzymes (1992), Academic Press, New York 1-61
2. Fersht A. Enzyme Structure and Mechanism. 2nd ed. (1985), W. H. Freeman, New York
3. Tissier A., McDonald J.P., Frank E.G., and Woodgate R. Polι, a remarkably error-prone human DNA polymerase. Genes Dev. 14 (2000) 1642-1650
4. Beckman J., Kincaid K., Hocek M., Spratt T., Engels J., Cosstick R., and Kuchta R.D. Human DNA polymerase α uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity. Biochemistry 46 (2007) 448-460
5. Sheriff A., Motea E., Lee I., and Berdis A.J. Mechanism and dynamics of translesion DNA synthesis catalyzed by the Escherichia coli Klenow fragment. Biochemistry 47 (2008) 8527-8537
6. Werneburg B.G., Ahn J., Zhong X., Hondal R.J., Kraynov V.S., and Tsai M.-D. DNA polymerase β: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity. Biochemistry 35 (1996) 7041-7050
7. Shah A.M., Li S.-X., Anderson K.S., and Sweasy J.B. Y265H mutator mutant of DNA polymerase β. Proper geometric alignment is critical for fidelity. J. Biol. Chem. 276 (2001) 10824-10831
8. Patel S.S., Wong I., and Johnson K.A. Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 30 (1991) 511-525
9. Capson T.L., Peliska J.A., Kaboord B.F., Frey M.W., Lively C., Dahlberg M., and Benkovic S.J. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4. Biochemistry 31 (1992) 10984-10994
10. Johnson K.A. Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates. Methods Enzymol. 249 (1995) 38-61
11. Joyce C.M., and Benkovic S.J. DNA polymerase fidelity: kinetics, structure, and checkpoints. Biochemistry 43 (2004) 14317-14324
12. Herschlag D., Piccirilli J.A., and Cech T.R. Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom. Biochemistry 30 (1991) 4844-4854
13. Kuchta R.D., Benkovic P., and Benkovic S.J. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 27 (1988) 6716-6725
14. Wong I., Patel S.S., and Johnson K.A. An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry 30 (1991) 526-537
15. Polesky A.H., Dahlberg M.E., Benkovic S.J., Grindley N.D.F., and Joyce C.M. Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. J. Biol. Chem. 267 (1992) 8417-8428
16. Dahlberg M.E., and Benkovic S.J. Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry 30 (1991) 4835-4843
17. Johnson K.A. Role of induced fit in enzyme specificity: a molecular forward/reverse switch. J. Biol. Chem. 283 (2008) 26297-26301
18. Tsai Y.-C., and Johnson K.A. A new paradigm for DNA polymerase specificity. Biochemistry 45 (2006) 9675-9687
19. Castro C., Smidansky E., Maksimchuk K.R., Arnold J.J., Korneeva V.S., Götte M., Konigsberg W., and Cameron C.E. Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 4267-4272
20. Castro C., Smidansky E.D., Arnold J.J., Maksimchuk K.R., Moustafa I., Uchida A., Gotte M., Konigsberg W., and Cameron C.E. Nucleic acid polymerases use a general acid for nucleotidyl transfer. Nat. Struct. Mol. Biol. 16 (2009) 212-218
21. Brautigam C.A., and Steitz T.A. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 8 (1998) 54-63
22. Zhong X., Patel S.S., and Tsai M.-D. DNA polymerase β. 5. Dissecting the functional roles of the two metal ions with Cr(III)dTTP. J. Am. Chem. Soc. 120 (1998) 235-236
23. Arndt J.W., Gong W., Zhong X., Showalter A.K., Liu J., Dunlap C.A., Lin Z., Paxson C., Tsai M.-D., and Chan M.K. Insight into the catalytic mechanism of DNA polymerase β: structures of intermediate complexes. Biochemistry 40 (2001) 5368-5375
24. Rachofsky E.L., Osman R., and Ross J.B. Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence. Biochemistry 40 (2001) 946-956
25. Fidalgo da Silva E., Mandal S.S., and Reha-Krantz L.J. Using 2-aminopurine fluorescence to measure incorporation of incorrect nucleotides by wild type and mutant bacteriophage T4 DNA polymerases. J. Biol. Chem. 277 (2002) 40640-40649
26. Purohit V., Grindley N.D.F., and Joyce C.M. Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I, Klenow fragment. Biochemistry 42 (2003) 10200-10211
27. DeLucia A.M., Grindley N.D.F., and Joyce C.M. Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence. Biochemistry 46 (2007) 10790-10803
28. Zhang H., Cao W., Zakharova E., Konigsberg W., and De La Cruz E.M. Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates. Nucleic Acids Res. 35 (2007) 6052-6062
29. Joyce C.M., Potapova O., Delucia A.M., Huang X., Basu V.P., and Grindley N.D.F. Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity. Biochemistry 47 (2008) 6103-6116
30. Johnson S.J., Taylor J.S., and Beese L.S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 3895-3900
31. Dunlap C.A., and Tsai M.-D. Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase β. Biochemistry 41 (2002) 11226-11235
32. Tippin B., Kobayashi S., Bertram J.G., and Goodman M.F. To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases. J. Biol. Chem. 279 (2004) 45360-45368
33. Doublié S., Sawaya M.R., and Ellenberger T. An open and closed case for all polymerases. Structure 7 (1999) R31-R35
34. Kuchta R.D., Mizrahi V., Benkovic P.A., Johnson K.A., and Benkovic S.J. Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 26 (1987) 8410-8417
35. Rothwell P.J., Mitaksov V., and Waksman G. Motions of the fingers subdomain of Klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases. Mol. Cell 19 (2005) 345-355
36. Stengel G., Gill J.P., Sandin P., Wilhelmsson L.M., Albinsson B., Norden B., and Millar D. Conformational dynamics of DNA polymerase probed with a novel fluorescent DNA base analogue. Biochemistry 46 (2007) 12289-12297
37. Allen W.J., Rothwell P.J., and Waksman G. An intramolecular FRET system monitors fingers subdomain opening in Klentaq1. Protein Sci. 17 (2008) 401-408
38. Luo G., Wang M., Konigsberg W.H., and Xie X.S. Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 12610-12615
39. Beckman J.W., Wang Q., and Guengerich F.P. Kinetic analysis of correct nucleotide insertion by a Y-family DNA polymerase reveals conformational changes both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence. J. Biol. Chem. 283 (2008) 36711-36723
40. Hanes J.W., Thal D.M., and Johnson K.A. Incorporation and replication of 8-oxo-deoxyguanosine by the human mitochondrial DNA polymerase. J. Biol. Chem. 281 (2006) 36241-36248
41. Barshop B.A., Wrenn R.F., and Frieden C. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM - a flexible, portable system. Anal. Biochem. 130 (1983) 134-145
42. Wachsstock D.H., and Pollard T.D. Transient state kinetics tutorial using the kinetics simulation program, KINSIM. Biophys. J. 67 (1994) 1260-1273
43. Johnson K.A., Simpson Z.B., and Blom T. Global Kinetic Explorer: a new computer program for dynamic simulation and fitting of kinetic data. Anal. Biochem. 387 (2009) 20-29
44. Kapanidis A.N., Heilemann M., Margeat E., Kong X., Nir E., and Weiss S. Alternating laser excitation of single molecules. In: Selvin P.R., and Ha T. (Eds). Single-Molecule Techniques: A Laboratory Manual (2008), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 85-119