17
Views
57
CrossRef citations to date
0
Altmetric
Chromosome Structure and Dynamics

Mechanism of Efficient and Accurate Nucleotide Incorporation Opposite 7,8-Dihydro-8-Oxoguanine by Saccharomyces cerevisiae DNA Polymerase η

&
Pages 2169-2176 | Received 12 Nov 2004, Accepted 08 Dec 2004, Published online: 27 Mar 2023

REFERENCES

  • Beckman, K. B., and B. N. Ames. 1997. Oxidative decay of DNA. J. Biol. Chem. 272:19633–19636.
  • Brieba, L. G., B. F. Eichman, R. J. Kokoska, S. Doublie, T. A. Kunkel, and T. Ellenberger. 2004. Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. EMBO J. 23:3452–3461.
  • Capson, T. L., J. A. Peliska, B. F. Kaboord, M. W. Frey, C. Lively, M. Dahlberg, and S. J. Benkovic. 1992. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4. Biochemistry 31:10984–10994.
  • Creighton, S., L. B. Bloom, and M. F. Goodman. 1995. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods Enzymol. 262:232–256.
  • Dahlberg, M. E., and S. J. Benkovic. 1991. Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry 30:4835–4843.
  • Einolf, H. J., and F. P. Guengerich. 2001. Fidelity of nucleotide insertion at 8-oxo-7,8-dihydroguanine by mammalian DNA polymerase δ. Steady-state and pre-steady state kinetic analysis. J. Biol. Chem. 276:3764–3771.
  • Fiala, K. A., and Z. Suo. 2004. Mechanism of DNA polymerization catalyzed by Sulfolobus solfataricus P2 DNA polymerase IV. Biochemistry 43:2116–2125.
  • Fiala, K. A., and Z. Suo. 2004. Pre-steady state kinetic studies of the fidelity of Sulfolobus solfataricus P2 DNA polymerase IV. Biochemistry 43:2106–2115.
  • Freisinger, E., A. P. Grollman, H. Miller, and C. Kisker. 2004. Lesion (in)tolerance reveals insights into DNA replication fidelity. EMBO J. 23:1494–1505.
  • Furge, L. L., and F. P. Guengerich. 1997. Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exo− and human immunodeficiency virus-1 reverse transcriptase using steady state and pre-steady state kinetics. Biochemistry 36:6475–6487.
  • Furge, L. L., and F. P. Guengerich. 1999. Explanation of pre-steady state kinetics and decreased burst amplitude of HIV-1 reverse transcriptase at sites of modified DNA bases with an additional, nonproductive enzyme-DNA-nucleotide complex. Biochemistry 38:4818–4825.
  • Graves, S. W., A. A. Johnson, and K. A. Johnson. 1998. Expression, purification, and initial kinetic characterization of the large subunit of the human mitochondrial DNA polymerase. Biochemistry 37:6050–6058.
  • Haracska, L., S. L. Yu, R. E. Johnson, L. Prakash, and S. Prakash. 2000. Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase η. Nat. Genet. 25:458–461.
  • Helbock, H. J., K. B. Beckman, M. K. Shigenaga, P. B. Walter, A. A. Woodall, H. C. Yeo, and B. N. Ames. 1998. DNA oxidation matters: the HPLC-electrochemical detection assay of 8-oxodeoxyguanosine and 8-oxoguanine. Proc. Natl. Acad. Sci. USA 95:288–293.
  • Hsu, G. W., M. Ober, T. Carell, and L. S. Beese. 2004. Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature 431:217–221.
  • Johnson, K. A. 1992. Transient-state kinetic analysis of enzyme reaction pathway. Enzymes XX:1–61.
  • Johnson, K. A. 1995. Rapid quench kinetic analysis of polymerases, adenosine triphosphatases, and enzyme intermediates. Methods Enzymol. 249:38–61.
  • Johnson, R. E., C. M. Kondratick, S. Prakash, and L. Prakash. 1999. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285:263–265.
  • Johnson, R. E., M. T. Washington, S. Prakash, and L. Prakash. 2000. Fidelity of human DNA polymerase η. J. Biol. Chem. 275:7447–7450.
  • Johnson, R. E., S. Prakash, and L. Prakash. 1999. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Polη. Science 283:1001–1004.
  • Johnson, R. E., S. Prakash, and L. Prakash. 1999. Requirement of DNA polymerase activity of yeast Rad30 protein for its biological function. J. Biol. Chem. 274:15975–15977.
  • Kouchakdjian, M., B. Verraiah, S. Shibutani, M. Eisenberg, F. Johnson, A. P. Grollman, and D. J. Patel. 1991. NMR structural studies of the ionizing radiation adduct 7-hydroxy-8-oxodeoxyguanosine (8-oxo-tH-dG) opposite deoxyadenosine in a DNA duplex. 8-oxo-7H-dG(syn) · dA(anti) alignment at lesion site. Biochemistry 30:1403–1412.
  • Krahn, J. M., W. A. Beard, H. Miller, A. P. Grollman, and S. H. Wilson. 2003. Structure of DNA polymerase β with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure 11:121–127.
  • Kuchta, R. D., V. Mizrahi, P. A. Benkovic, K. A. Johnson, and S. J. Benkovic. 1987. Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 26:8410–8417.
  • Lipscomb, L. A., M. E. Peek, M. L. Morningstar, S. M. Verghis, E. M. Miller, A. Rich, J. M. Essigmann, and L. D. Williams. 1995. X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine. Proc. Natl. Acad. Sci. USA 92:719–723.
  • Lowe, L. G., and F. P. Guengerich. 1996. Steady state and pre-steady state kinetic analysis of dNTP insertion opposite 8-oxo-7,8-dihydroguanine by Escherichia coli polymerases I exo− and II exo−. Biochemistry 35:9840–9849.
  • Masutani, C., R. Kusumoto, A. Yamada, N. Dohmae, M. Yokoi, M. Yuasa, M. Araki, S. Iwai, K. Takio, and F. Hanaoka. 1999. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Nature 399:700–704.
  • Matsuda, T., K. Bebenek, C. Matsutani, F. Hanaoka, and T. A. Kunkel. 2000. Low fidelity of DNA synthesis by human DNA polymerase η. Nature 404:1011–1013.
  • McAuley-Hecht, K. E., G. A. Leonard, N. J. Gibson, J. B. Thomson, W. P. Watson, W. N. Hunter, and T. Brown. 1994. Crystal structure of a DNA duplex containing 8-hydrodeoxyguanine-adenine base pairs. Biochemistry 33:10266–10270.
  • McDonald, J. P., A. S. Levine, and R. Woodgate. 1997. The Saccharomyces cerevisiae RAD30 gene, a homologue of Escherichia coli dinB and umuC, is DNA damage inducible and functions in a novel error-free postreplication repair mechanism. Genetics 147:1557–1568.
  • Miller, H., R. Prasad, S. H. Wilson, F. Johnson, and A. P. Grollman. 2000. 8-Oxo-dGTP incorporation by DNA polymerase β is modified by active-site residue Asn279. Biochemistry 39:1029–1033.
  • Mizrahi, V., R. N. Henrie, J. F. Marlier, K. A. Johnson, and S. J. Benkovic. 1985. Rate-limiting steps in the DNA polymerase I reaction pathway. Biochemistry 24:4010–4018.
  • Moriya, M. 1993. Single-stranded shuttle phagemid for mutagenesis studies in mammalian cells: 8-oxoguanine in DNA induced targeted G · C→T · A transversions in simian kidney cells. Proc. Natl. Acad. Sci. USA 90:1122–1126.
  • Oda, Y., S. Uesugi, M. Ikehara, S. Nishimura, Y. Kawase, H. Ishikawa, H. Inoue, and E. Ohtsuda. 1991. NMR studies of a DNA containing 8-hydroxydeoxyguanosine. Nucleic Acid Res. 19:1407–1412.
  • Patel, S. S., I. Wong, and K. A. Johnson. 1991. Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 30:511–525.
  • Roettger, M. P., K. A. Fiala, S. Sompalli, Y. Dong, and Z. Suo. 2004. Pre-steady state kinetic studies of the fidelity of human DNA polymerase μ. Biochemistry 43:13827–13838.
  • Roush, A. A., M. Suarez, E. C. Friedberg, M. Radman, and W. Siede. 1998. Deletion of the Saccharomyces cerevisiae gene RAD30 encoding an Escherichia coli DinB homolog confers UV radiation sensitivity and altered mutability. Mol. Gen. Genet. 257:686–692.
  • Shibutani, S., M. Takeshita, and A. P. Grollman. 1991. Insertions of specific bases during DNA synthesis past the oxidation-damaged base 8-oxo-dG. Nature 349:431–434.
  • Sun, L., K. Zhou, P. Hohler, E. T. Kool, F. Yuan, Z. Wang, and J. S. Taylor. 2003. Yeast Pol η holds a cis-syn thymine dimer loosely in the active site during elongation opposite the 3′-T of the dimer, but tightly opposite the 5′-T. Biochemistry 42:9431–9437.
  • Trincao, J., R. E. Johnson, C. R. Escalante, S. Prakash, L. Prakash, and A. K. Aggarwal. 2001. Structure of the catalytic core of S. cerevisiae DNA polymerase η: implications for translesion DNA synthesis. Mol. Cell 8:417–426.
  • Vaisman, A., and R. Woodgate. 2001. Unique misinsertion specificity of polι may decrease the mutagenic potential of deaminated cytosines. EMBO J. 20:6520–6529.
  • Washington, M. T., L. Prakash, and S. Prakash. 2001. Yeast DNA polymerase η utilizes an induced-fit mechanism of nucleotide incorporation. Cell 107:917–927.
  • Washington, M. T., L. Prakash, and S. Prakash. 2003. Mechanism of nucleotide incorporation opposite a thymine-thymine dimer by yeast DNA polymerase η. Proc. Natl. Acad. Sci. USA 100:12093–12098.
  • Washington, M. T., R. E. Johnson, S. Prakash, and L. Prakash. 1999. Fidelity and processivity of Saccharomyces cerevisiae DNA polymerase η. J. Biol. Chem. 274:36835–36838.
  • Washington, M. T., R. E. Johnson, L. Prakash, and S. Prakash. 2003. The mechanism of nucleotide incorporation by human DNA polymerase η differs from that of the yeast enzyme. Mol. Cell. Biol. 23:8316–8322.
  • Washington, M. T., R. E. Johnson, L. Prakash, and S. Prakash. 2004. Human DNA polymerase ι utilizes different nucleotide incorporation mechanisms dependent upon the template base. Mol. Cell. Biol. 24:936–943.
  • Washington, M. T., R. E. Johnson, S. Prakash, and L. Prakash. 2000. Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase η. Proc. Natl. Acad. Sci. USA 97:3094–3099.
  • Werneburg, B. G., J. Ahn, X. Zhong, R. J. Hondal, V. S. Kraynov, and M. D. Tsai. 1996. DNA polymerase β: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity. Biochemistry 35:7041–7050.
  • Zhong, X., S. S. Patel, B. G. Werneburg, and M. D. Tsai. 1997. DNA polymerase β: multiple conformational changes in the mechanism of catalysis. Biochemistry 36:11891–11900.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.