Many environmental carcinogens, both chemical and physical, cause cancer at least in part by producing mutations, as evidenced by characteristic exposure-related mutation spectra in human cancers and cancers associated with genetic defects in DNA repair, as well as animal models. The focus of the proposed continuing investigations on interaction of DNA polymerases with carcinogen-modified DNA will be structure-function relationships. One focus will be biochemical and in vivo studies with the DNA polymerases of a model organism, the crenarcheon Sulfolobus solfataricus, and approaches will be extended to human Y- family polymerases. (1) Structural and functional studies will be done on the four DNA polymerases of S. solfataricus, Dpo1, Dpo2, Dpo3, and Dpo4, including their roles in normal replication and past several DNA adducts, as well as defining the role of the heterotrimeric PCNA protein in this organism. Structures of these polymerases will be determined by X-ray crystallography (including PCNA complexes) and motions of individual parts will be analyzed using hydrogen-deuterium (H-D) exchange rates. A major goal is understanding trafficking of these four DNA polymerases at adduct-blocked replication forks, as a model for other systems. The in vivo functions of the polymerases will be determined using quantitation of proteins, transgenic knockouts, immunoprecipitation of polymerase partners, and site-specific mutagenesis of specific DNA adducts. (2) Analysis of microscopic events in catalysis by two model DNA polymerases will be done using rapid fluorescence kinetics (Dpo4 tryptophan mutants and a coumarin-labeled bacteriophage T7 polymerase mutant) and H-D exchange kinetics (Dpo4), with a view to events in incorporation opposite DNA adducts. (3) Structure-function relationships will be analyzed in recombinant human Y-family DNA polymerases using catalytically-active truncated versions of human pol 7, 9, and: using approaches developed with the Dpo polymerases, including X-ray crystallography, pre-steady-state kinetics, and H-D exchange kinetics. Collectively, these studies have the goal of extending the understanding of how important DNA polymerases catalyze correct and incorrect insertions and respond to DNA blocks, phenomena relevant to cancer.
Many of the chemicals that cause cancer do so by binding to the DNA in the cells of the body. When this genetic material (damaged DNA) is copied by enzyme systems in the body called DNA polymerases, mistakes may occur (mutations) and lead to cancer. The goals of this project involve understanding how the DNA polymerases make such mistakes.
|O'Flaherty, Derek K; Guengerich, F Peter (2014) Steady-state kinetic analysis of DNA polymerase single-nucleotide incorporation products. Curr Protoc Nucleic Acid Chem 59:7.21.1-7.21.13|
|Zhao, Linlin; Pence, Matthew G; Eoff, Robert L et al. (2014) Elucidation of kinetic mechanisms of human translesion DNA polymerase ? using tryptophan mutants. FEBS J 281:4394-410|
|Kim, Jinsook; Song, Insil; Jo, Ara et al. (2014) Biochemical analysis of six genetic variants of error-prone human DNA polymerase ? involved in translesion DNA synthesis. Chem Res Toxicol 27:1837-52|
|Patra, Amritraj; Nagy, Leslie D; Zhang, Qianqian et al. (2014) Kinetics, structure, and mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine bypass by human DNA polymerase ?. J Biol Chem 289:16867-82|
|Stornetta, Alessia; Angelov, Todor; Guengerich, F Peter et al. (2013) Incorporation of nucleoside probes opposite Oýýý-methylguanine by Sulfolobus solfataricus DNA polymerase Dpo4: importance of hydrogen bonding. Chembiochem 14:1634-9|
|Zhao, Linlin; Christov, Plamen P; Kozekov, Ivan D et al. (2012) Replication of N2,3-ethenoguanine by DNA polymerases. Angew Chem Int Ed Engl 51:5466-9|
|Choi, Jeong-Yun; Eoff, Robert L; Pence, Matthew G et al. (2011) Roles of the four DNA polymerases of the crenarchaeon Sulfolobus solfataricus and accessory proteins in DNA replication. J Biol Chem 286:31180-93|
|Chowdhury, Goutam; Guengerich, F Peter (2011) Liquid chromatography-mass spectrometry analysis of DNA polymerase reaction products. Curr Protoc Nucleic Acid Chem Chapter 7:Unit 7.16.1-11|
|Shanmugam, Ganesh; Kozekov, Ivan D; Guengerich, F Peter et al. (2011) 1,N2-Etheno-2'-deoxyguanosine adopts the syn conformation about the glycosyl bond when mismatched with deoxyadenosine. Chem Res Toxicol 24:1071-9|
|Irimia, Adriana; Loukachevitch, Lioudmila V; Eoff, Robert L et al. (2010) Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1013-8|
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