Chapter 28

Where to Start

O’Donnell, M., Langston, L. and Stillman, B. 2013. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb. Perspect. Biol. 5:1–13.

Johnson, A., and O’Donnell, M. 2005. Cellular DNA replicases: Components and dynamics at the replication fork. Annu. Rev. Biochem. 74:283–315.

Kornberg, A. 1988. DNA replication. J. Biol. Chem. 263:1–4.

Wang, J. C. 1982. DNA topoisomerases. Sci. Am. 247(1):94–109.

Lindahl, T. 1993. Instability and decay of the primary structure of DNA. Nature 362:709–715.

Greider, C. W., and Blackburn, E. H. 1996. Telomeres, telomerase, and cancer. Sci. Am. 274(2):92–97.

Books

Kornberg, A., and Baker, T. A. 1992. DNA Replication (2d ed.). W. H. Freeman and Company.

Bloomfield, V. A., Crothers, D., Tinoco, I., and Hearst, J. 2000. Nucleic Acids: Structures, Properties and Functions. University Science Books.

Friedberg, E. C., Walker, G. C., and Siede, W. 1995. DNA Repair and Mutagenesis. American Society for Microbiology.

Cozzarelli, N. R., and Wang, J. C. (Eds.). 1990. DNA Topology and Its Biological Effects. Cold Spring Harbor Laboratory Press.

DNA Topology and Topoisomerases

Graille, M., Cladiere, L., Durand, D., Lecointe, F., Gadelle, D., Quevillon-Cheruel, S., Vachette, P., Forterre, P., and van Tilbeurgh, H. 2008. Crystal structure of an intact type II DNA topoisomerase: Insights into DNA transfer mechanisms. Structure 16:360–370.

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Charvin, G., Strick, T. R., Bensimon, D., and Croquette, V. 2005. Tracking topoisomerase activity at the single-molecule level. Annu. Rev. Biophys. Biomol. Struct. 34:201–219.

Sikder, D., Unniraman, S., Bhaduri, T., and Nagaraja, V. 2001. Functional cooperation between topoisomerase I and single strand DNA-binding protein. J. Mol. Biol. 306:669–679.

Fortune, J. M., and Osheroff, N. 2000. Topoisomerase II as a target for anticancer drugs: When enzymes stop being nice. Prog. Nucleic Acid Res. Mol. Biol. 64:221–253.

Isaacs, R. J., Davies, S. L., Sandri, M. I., Redwood, C., Wells, N. J., and Hickson, I. D. 1998. Physiological regulation of eukaryotic topoisomerase II. Biochim. Biophys. Acta 1400:121–137.

Wang, J. C. 1998. Moving one DNA double helix through another by a type II DNA topoisomerase: The story of a simple molecular machine. Q. Rev. Biophys. 31:107–144.

Baird, C. L., Harkins, T. T., Morris, S. K., and Lindsley, J. E. 1999. Topoisomerase II drives DNA transport by hydrolyzing one ATP. Proc. Natl. Acad. Sci. U.S.A. 96:13685–13690.

Vologodskii, A. V., Levene, S. D., Klenin, K. V., Frank, K. M., and Cozzarelli, N. R. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227:1224–1243.

Fisher, L. M., Austin, C. A., Hopewell, R., Margerrison, M., Oram, M., Patel, S., Wigley, D. B., Davies, G. J., Dodson, E. J., Maxwell, A., et al. 1991. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351:624–629.

Mechanism of Replication

Davey, M. J., and O’Donnell, M. 2000. Mechanisms of DNA replication. Curr. Opin. Chem. Biol. 4:581–586.

Keck, J. L., and Berger, J. M. 2000. DNA replication at high resolution. Chem. Biol. 7:R63–R71.

Kunkel, T. A., and Bebenek, K. 2000. DNA replication fidelity. Annu. Rev. Biochem. 69:497–529.

Waga, S., and Stillman, B. 1998. The DNA replication fork in eukaryotic cells. Annu. Rev. Biochem. 67:721–751.

Marians, K. J. 1992. Prokaryotic DNA replication. Annu. Rev. Biochem. 61:673–719.

DNA Polymerases and Other Enzymes of Replication

Kurth, I., and O’Donnell, M. 2013. New insights into replisome fluidity during chromosome replication. Trends Biochem. Sci. 38:195–203.

Nandakumar, J., and Cech, T. R. 2013. Finding the end: Recruitment of telomerase to telomeres. Nat. Rev. Mol. Cell. Biol. 14:69–82.

Singleton, M. R., Sawaya, M. R., Ellenberger, T., and Wigley, D. B. 2000. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 101:589–600.

Donmez, I., and Patel, S. S. 2006. Mechanisms of a ring shaped helicase. Nucleic Acids Res. 34:4216–4224.

Johnson, D. S., Bai, L., Smith, B. Y., Patel, S. S., and Wang, M. D. 2007. Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell 129:1299–1309.

Lee, S. J., Qimron, U., and Richardson, C. C. 2008. Communication between subunits critical to DNA binding by hexameric helicase of bacteriophage T7. Proc. Natl. Acad. Sci. U.S.A. 105:8908–8913.

Toth, E. A., Li, Y., Sawaya, M. R., Cheng, Y., and Ellenberger, T. 2003. The crystal structure of the bifunctional primase-helicase of bacteriophage T7. Mol. Cell 12:1113–1123.

Hubscher, U., Maga, G., and Spadari, S. 2002. Eukaryotic DNA polymerases. Annu. Rev. Biochem. 71:133–163.

Doublié, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. 1998. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391:251–258.

Arezi, B., and Kuchta, R. D. 2000. Eukaryotic DNA primase. Trends Biochem. Sci. 25:572–576.

Jager, J., and Pata, J. D. 1999. Getting a grip: Polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 9:21–28.

Steitz, T. A. 1999. DNA polymerases: Structural diversity and common mechanisms. J. Biol. Chem. 274:17395–17398.

Beese, L. S., Derbyshire, V., and Steitz, T. A. 1993. Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260:352–355.

McHenry, C. S. 1991. DNA polymerase III holoenzyme: Components, structure, and mechanism of a true replicative complex. J. Biol. Chem. 266:19127–19130.

Kong, X. P., Onrust, R., O’Donnell, M., and Kuriyan, J. 1992. Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp. Cell 69: 425–437.

Polesky, A. H., Steitz, T. A., Grindley, N. D., and Joyce, C. M. 1990. Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. J. Biol. Chem. 265:14579–14591.

Lee, J. Y., Chang, C., Song, H. K., Moon, J., Yang, J. K., Kim, H. K., Kwon, S. T., and Suh, S. W. 2000. Crystal structure of NAD+ dependent DNA ligase: Modular architecture and functional implications. EMBO J. 19:1119–1129.

Timson, D. J., and Wigley, D. B. 1999. Functional domains of an NAD+-dependent DNA ligase. J. Mol. Biol. 285:73–83.

Doherty, A. J., and Wigley, D. B. 1999. Functional domains of an ATP-dependent DNA ligase. J. Mol. Biol. 285:63–71.

von Hippel, P. H., and Delagoutte, E. 2001. A general model for nucleic acid helicases and their “coupling” within macromolecular machines. Cell 104:177–190.

Tye, B. K., and Sawyer, S. 2000. The hexameric eukaryotic MCM helicase: Building symmetry from nonidentical parts. J. Biol. Chem. 275:34833–34836.

Marians, K. J. 2000. Crawling and wiggling on DNA: Structural insights to the mechanism of DNA unwinding by helicases. Struct. Fold. Des. 5:R227–R235.

Soultanas, P., and Wigley, D. B. 2000. DNA helicases: “Inching forward.” Curr. Opin. Struct. Biol. 10:124–128.

de Lange, T. 2009. How telomeres solve the end-protection problem. Science 326:948–952.

Bachand, F., and Autexier, C. 2001. Functional regions of human telomerase reverse transcriptase and human telomerase RNA required for telomerase activity and RNA-protein interactions. Mol. Cell Biol. 21:1888–1897.

Griffith, J. D., Comeau, L., Rosenfield, S., Stansel, R. M., Bianchi, A., Moss, H., and de Lange, T. 1999. Mammalian telomeres end in a large duplex loop. Cell 97:503–514.

McEachern, M. J., Krauskopf, A., and Blackburn, E. H. 2000. Telomeres and their control. Annu. Rev. Genet. 34:331–358.

Mutations and DNA Repair

Yang, W. 2003. Damage repair DNA polymerases Y. Curr. Opin. Struct. Biol. 13:23–30.

Wood, R. D., Mitchell, M., Sgouros, J., and Lindahl, T. 2001. Human DNA repair genes. Science 291:1284–1289.

Shin, D. S., Chahwan, C., Huffman, J. L., and Tainer, J. A. 2004. Structure and function of the double-strand break repair machinery. DNA Repair (Amst.) 3:863–873.

Michelson, R. J., and Weinert, T. 2000. Closing the gaps among a web of DNA repair disorders. BioEssays 22:966–969.

Aravind, L., Walker, D. R., and Koonin, E. V. 1999. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27:1223–1242.

Mol, C. D., Parikh, S. S., Putnam, C. D., Lo, T. P., and Tainer, J. A. 1999. DNA repair mechanisms for the recognition and removal of damaged DNA bases. Annu. Rev. Biophys. Biomol. Struct. 28:101–128.

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Parikh, S. S., Mol, C. D., and Tainer, J. A. 1997. Base excision repair enzyme family portrait: Integrating the structure and chemistry of an entire DNA repair pathway. Structure 5:1543–1550.

Vassylyev, D. G., and Morikawa, K. 1997. DNA-repair enzymes. Curr. Opin. Struct. Biol. 7:103–109.

Verdine, G. L., and Bruner, S. D. 1997. How do DNA repair proteins locate damaged bases in the genome? Chem. Biol. 4:329–334.

Bowater, R. P., and Wells, R. D. 2000. The intrinsically unstable life of DNA triplet repeats associated with human hereditary disorders. Prog. Nucleic Acid Res. Mol. Biol. 66:159–202.

Cummings, C. J., and Zoghbi, H. Y. 2000. Fourteen and counting: Unraveling trinucleotide repeat diseases. Hum. Mol. Genet. 9: 909–916.

Defective DNA Repair and Cancer

Dever, S. M., White, E. R., Hartman, M. C., and Valerie, K. 2012. BRCA1-directed, enhanced and aberrant homologous recombination: Mechanism and potential treatment strategies. Cell Cycle 11:687–94.

Berneburg, M., and Lehmann, A. R. 2001. Xeroderma pigmentosum and related disorders: Defects in DNA repair and transcription. Adv. Genet. 43:71–102.

Lambert, M. W., and Lambert, W. C. 1999. DNA repair and chromatin structure in genetic diseases. Prog. Nucleic Acid Res. Mol. Biol. 63:257–310.

Buys, C. H. 2000. Telomeres, telomerase, and cancer. New Engl. J. Med. 342:1282–1283.

Urquidi, V., Tarin, D., and Goodison, S. 2000. Role of telomerase in cell senescence and oncogenesis. Annu. Rev. Med. 51:65–79.

Lynch, H. T., Smyrk, T. C., Watson, P., Lanspa, S. J., Lynch, J. F., Lynch, P. M., Cavalieri, R. J., and Boland, C. R. 1993. Genetics, natural history, tumor spectrum, and pathology of hereditary nonpolyposis colorectal cancer: An updated review. Gastroenterology 104:1535–1549.

Fishel, R., Lescoe, M. K., Rao, M. R. S., Copeland, N. G., Jenkins, N. A., Garber, J., Kane, M., and Kolodner, R. 1993. The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75:1027–1038.

Ames, B. N., and Gold, L. S. 1991. Endogenous mutagens and the causes of aging and cancer. Mutat. Res. 250:3–16.

Ames, B. N. 1979. Identifying environmental chemicals causing mutations and cancer. Science 204:587–593.

Recombination and Recombinases

Singleton, M. R., Dillingham, M. S., Gaudier, M., Kowalczykowski, S. C., and Wigley, D. B. 2004. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432: 187–193.

Spies, M., Bianco, P. R., Dillingham, M. S., Handa, N., Baskin, R. J., and Kowalczykowski, S. C. 2003. A molecular throttle: The recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 114:647–654.

Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25:1562165.

Prevost, C., and Takahashi, M. 2003. Geometry of the DNA strands within the RecA nucleofilament: Role in homologous recombination. Q. Rev. Biophys. 36:429–453.

Van Duyne, G. D. 2001. A structural view of Cre-loxP site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30:87–104.

Chen, Y., Narendra, U., Iype, L. E., Cox, M. M., and Rice, P. A. 2000. Crystal structure of a Flp recombinase-Holliday junction complex: Assembly of an active oligomer by helix swapping. Mol. Cell 6:885–897.

Craig, N. L. 1997. Target site selection in transposition. Annu. Rev. Biochem. 66:437–474.

Gopaul, D. N., Guo, F., and Van Duyne, G. D. 1998. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:4175–4187.

Gopaul, D. N., and Van Duyne, G. D. 1999. Structure and mechanism in site-specific recombination. Curr. Opin. Struct. Biol. 9:14–20.