Mechanisms of DNA Repair

Biochemistry 201

Advanced Molecular Biology

January 24 and 26, 2000

Mechanisms of DNA Repair Handout

Mechanisms of DNA Repair Slides

Professor Gil Chu

Useful Review Articles

I. Robert Lehman (1997) Eukaryotic DNA Repair Minireview Series. J. Biol. Chem. 272: 23463.

Chu G. & Mayne, L. (1996) Xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy: do the genes explain the diseases? Trends Genet. 12, 187-192.

Croteau DL and Bohr VA (1997) Repair of oxidative damage to nuclear and mitochondrial DNA in mammalian cells. J. Biol. Chem. 272, 25409-25412.

Gilbert Chu (1997). Double Strand Break Repair J. Biol. Chem. 272, 24097-24100.

Paul Modrich (1997). Strand-specific Mismatch Repair in Mammalian Cells. J. Biol. Chem. 272, 24727-24730.

Richard D. Wood (1997) Nucleotide Excision Repair in Mammalian Cells. J. Biol. Chem. 272, 23465-23468.

Recommended Texts

Friedberg, E. C., Walker, G. C & Siede, W. (1995). DNA Repair and Mutagenesis, ASM Press, Washington D.C. 698 pages.,

Nickoloff, J. A. and Hoekstra, M. F. (1998) DNA Damage & Repair, Volume 1: DNA Repair in Prokaryotes and Lower Eukaryotes, Humana Press, Totowa New Jersey.

Nickoloff, J. A. and Hoekstra, M. F. (1998) DNA Damage & Repair, Volume 2: DNA Repair in Higher Eukaryotes, Humana Press, Totowa New Jersey 639 pages.

Gil Chu's References

Literature References

Ban, C., Junop, M., Yang, W. (1999) Transformation of MutL by ATP Binding and Hydrolysis: A Switch in DNA Mismatch Repair. Cell, Vol. 97, 85-97.

Ban C, Yang W. (1998). Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis. Cell 95(4):541-52.

Bohr V, Phillips D, Hanawalt P: Heterogeneous DNA damage and repair in the mammlian genome. Cancer Res. 47: 6426-6436, 1987

Bridges BA (1998) DNA repair: getting past a lesion - at a cost. Curr Biol 8(24):R886-8. Review.

Chu G, Chang E: Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA. Science 242: 564-567, 1988

Chu G (1997) Double strand break repair. J Biol Chem 272(39):24097-100.

Cleaver JE, Kraemer KH. Xeroderma pigmentosum. In: Scriver CR, Beaudet AL, Sly WS, Valle D (ed.): The Metabolic Basis of Inherited Disease. New York: McGraw-Hill, 1989, pp 2949-2971

Friedberg E: Deoxyribonucleic acid repair in the yeast Saccharomyces cerevisiae. Microbiol. Rev. 52: 70-102, 1988

Goodman M. F. (1998). Purposeful mutations.Nature 395(6699):221, 223.

Grawunder U, Zimmer D, Kulesza P, Lieber MR (1998). Requirement for an interaction of XRCC4 with DNA ligase IV for wild-type V(D)J recombination and DNA double-strand break repair in vivo.J Biol Chem 1998 Sep 18;273(38):24708-14.

Holmes,A. M. & Haber, J. E. (1999). Double-Strand Break Repair in Yeast Requires Both Leading and Lagging Strand DNA Polymerases Cell, Vol. 96, 415-424.

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Hosfield, D. J., Mol1, C. D., Shen, B. H. & Tainer, J. A. (1998) Structure of the DNA Repair and Replication Endonuclease and Exonuclease FEN-1: Coupling DNA and PCNA Binding to FEN-1 Activity Cell, Vol. 95, 135-146.

Johnson RE, Prakash S, Prakash L. (1999). Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Pol-eta.Science 283(5404):1001-4.

Kang, S., Lee, H., Han, J. S. and Hwang, D. S. (1999) Interaction of SeqA and Dam Methylase on the Hemimethylated Origin of Escherichia coli Chromosomal DNA Replication. J. Biol. Chem. 274 11463-11468.

Lahue, R. S., Au, K. G. and Modrich, P. (1989). DNA Mismatch Correction in a Defined System. Science 245, 160-164.

Li, S. and Smerdon, M. J. (1999). Base Excision Repair of N-Methylpurines in a Yeast Minichromosome. EFFECTS OF TRANSCRIPTION, DNA SEQUENCE, AND NUCLEOSOME POSITIONING. J. Biol. Chem. 1999;274 12201-12204.

Lindahl, T., Sedgwick, B., Sekiguchi, M., and Nakabeppu, Y. (1988). Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 57, 133-157.

Modrich, P. (1987). DNA mismatch correction. Annu. Rev. Biochem. 56, 435-466.

Modrich, P. (1989). Methyl-directed DNA Mismatch Correction. J. Biol. Chem., 264(12), 6597-6600.

Modrich P. (1997). Strand-specific mismatch repair in mammalian cells. J Biol Chem 272(40):24727-30

Paz-Elizur T, Takeshita M, Goodman M, O'Donnell M, Livneh Z. (1996). Mechanism of translesion DNA synthesis by DNA polymerase II. Comparison to DNA polymerases I and III core.J Biol Chem 271(40):24662-9.

Reuven,N. B., Tomer, G. and Livneh, Z. (1998), The Mutagenesis Proteins UmuD9 and UmuC Prevent Lethal Frameshifts While Increasing Base Substitution Mutations. Molecular Cell, Vol. 2, 191&endash;199.

Sancar, A., and Sancar, G. B. (1988). DNA repair enzymes. Annu. Rev. Biochem. 57, 29-67.

Sancar G: DNA photolyases: physical properties, action mechanism, and roles in DNA repair. Mutation Res. 236:147-160,1990

Skaliter R, Paz-Elizur T, Livneh Z (1996). A smaller form of the sliding clamp subunit of DNA polymerase III is induced by UV irradiation in Escherichia coli. J Biol Chem 271(5):2478-81.

Tanaka K, Miura N, Satokata I, et al: Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain. Nature 348: 73-76, 1990

Tomer G, Reuven NB, Livneh Z. (1998), The beta subunit sliding DNA clamp is responsible for unassisted mutagenic translesion replication by DNA polymerase III holoenzyme.Proc Natl Acad Sci U S A 95(24):14106-11.

van Duin M, deWit J, Odijk H, et al: Molecular characterization of the human excision repair gene EROC-1: cDNA cloning and amino acid homology with yeast DNA repair gene RADiO. Cell 44: 913-923, 1986.

Van Houten, B. (1990). Nucleotide excision repair in Escherichia coli. Microbiol Rev, 54(1), 18-51.

Weeda G, Van Ham R, Vermeulen W, et al: A presumed DNA helicase encoded by ERCC-3 is involved in the human repair disorders xeroderma pigmentosum and Cockayne's syndrome. Cell 62: 777-791,1990

Wood R, Robins P, Lindahl T: Complementation of the xeroderma pigmentosum DNA repair defect in cell free extracts. Cell 53: 97-106, 1988

Yamagata Y, Kato M, Odawara K, Tokuno Y, Nakashima Y, Matsushima N, Yasumura K, Tomita K, Ihara K, Fujii Y, Nakabeppu Y, Sekiguchi M, Fujii S. (1996). Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli. Cell 86(2):311-9.

Umar A, Buermeyer AB, Simon JA, Thomas DC, Clark AB, Liskay RM, Kunkel TA. (1996). Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell 87(1):65-73.

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