title: Human DNA polymerases catalyze lesion bypass across benzo[a]pyrene-derived DNA adduct clustered with an abasic site.
abstract: The combined action of oxidative stress and genotoxic polycyclic aromatic hydrocarbons derivatives can lead to cluster-type DNA damage that includes both a modified nucleotide and a bulky lesion. As an example, we investigated the possibility of repair of an AP site located opposite a minor groove-positioned (+)-trans-BPDE-dG or a base-displaced intercalated (+)-cis-BPDE-dG adduct (BP lesion) by a BER system. Oligonucleotides with single uracil residue in the certain position were annealed with complementary oligonucleotides bearing either a cis- or trans-BP adduct. Digestion with uracil DNA glycosylase was utilized to generate an AP site which was then hydrolyzed by APE1, and the resulting gap was processed by X-family DNA polymerases β (Polβ) and λ (Polλ), or Y-family polymerase ι (Polι). By varying reaction conditions, namely, Mg2+/Mn2+ replacement/combination and ionic strength decrease, we found that under certain conditions both Polβ and Polι can catalyze lesion bypass across both cis- and trans-BP adducts in the presence of physiological dNTP concentrations. Polβ and Polι catalyze gap filling trans-lesion synthesis in an error prone manner. By contrast, Polλ selectively introduced the correct dCTP opposite the modified dG in the case of cis-BP-dG adduct only, and did not bypass the stereoisomeric trans-adduct under any of the conditions examined. The results suggest that Polλ is a specialized polymerase that can process these kinds of lesions.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev av. 8, 630090 Novosibirsk, Russia.
authors.forename: Lidia V
authors.initials: LV
authors.lastname: Starostenko
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev av. 8, 630090 Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia.
authors.forename: Nadejda I
authors.initials: NI
authors.lastname: Rechkunova
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev av. 8, 630090 Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia.
authors.forename: Natalia A
authors.initials: NA
authors.lastname: Lebedeva
authors.affiliation: Department of Chemistry, New York University, 31 Washington Place/Suite 453 Brown New York, NY 10003-5180, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kolbanovskiy
authors.affiliation: Department of Chemistry, New York University, 31 Washington Place/Suite 453 Brown New York, NY 10003-5180, USA. Electronic address: ng1@nyu.edu.
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev av. 8, 630090 Novosibirsk, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia. Electronic address: lavrik@niboch.nsc.ru.
authors.forename: Olga I
authors.initials: OI
authors.lastname: Lavrik
mesh_terms: D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D001564:Benzo(a)pyrene / Q000737:chemistry / Q000378:metabolism*; D002384:Catalysis; D018736:DNA Adducts / Q000737:chemistry / Q000378:metabolism*; D004256:DNA Polymerase I / Q000737:chemistry / Q000378:metabolism; D019951:DNA Polymerase beta / Q000378:metabolism; D004260:DNA Repair; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism*; D003849:Deoxyguanosine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data
chemical_list: D018736:DNA Adducts; C056612:benzo(a)pyrene-DNA adduct; D001564:Benzo(a)pyrene; D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide; C040060:7,8-dihydroxy-9,10-epoxide-7,8,9,10-tetrahydrobenzo(a)pyrene-10-deoxyguanosine; C415367:DNA polymerase beta2; D004256:DNA Polymerase I; D019951:DNA Polymerase beta; D004259:DNA-Directed DNA Polymerase; D003849:Deoxyguanosine