title: Processing of the abasic sites clustered with the benzo[a]pyrene adducts by the base excision repair enzymes.
abstract: The major enzyme in eukaryotic cells that catalyzes the cleavage of apurinic/apyrimidinic (AP or abasic) sites is AP endonuclease 1 (APE1) that cleaves the phosphodiester bond on the 5'-side of AP sites. We found that the efficiency of AP site cleavage by APE1 was affected by the benzo[a]pyrenyl-DNA adduct (BPDE-dG) in the opposite strand. AP sites directly opposite of the modified dG or shifted toward the 5' direction were hydrolyzed by APE1 with an efficiency moderately lower than the AP site in the control DNA duplex, whereas AP sites shifted toward the 3' direction were hydrolyzed significantly less efficiently. For all DNA structures except DNA with the AP site shifted by 3 nucleotides in the 3' direction (AP+3-BP-DNA), hydrolysis was more efficient in the case of (+)-trans-BPDE-dG. Using molecular dynamic simulation, we have shown that in the complex of APE1 with the AP+3-BP-DNA, the BP residue is located within the DNA bend induced by APE1 and contacts the amino acids in the enzyme catalytic center and the catalytic metal ion. The geometry of the APE1 active site is perturbed more significantly by the trans-isomer of BPDE-dG that intercalates into the APE1-DNA complex near the cleaved phosphodiester bond. The ability of DNA polymerases β (Polβ), λ and ι to catalyze gap-filling synthesis in cooperation with APE1 was also analyzed. Polβ was shown to inhibit the 3'→5' exonuclease activity of APE1 when both enzymes were added simultaneously and to insert the correct nucleotide into the gap arising after AP site hydrolysis. Therefore, further evidence for the functional cooperation of APE1 and Polβ in base excision repair was obtained.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk, 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, Russia.
authors.forename: Lidia V
authors.initials: LV
authors.lastname: Starostenko
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk, 630090, Russia.
authors.forename: Nadejda I
authors.initials: NI
authors.lastname: Rechkunova
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk, 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, Russia.
authors.forename: Natalia A
authors.initials: NA
authors.lastname: Lebedeva
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk, 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, Russia.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Lomzov
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk, 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, Russia.
authors.forename: Vladimir V
authors.initials: VV
authors.lastname: Koval
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk, 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, 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 / Q000378:metabolism; D020134:Catalytic Domain; D018736:DNA Adducts / Q000378:metabolism*; D004249:DNA Damage; D019951:DNA Polymerase beta / Q000378:metabolism*; D004260:DNA Repair; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D000094769:DNA Polymerase iota
chemical_list: D018736:DNA Adducts; D015123:7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide; C415367:DNA polymerase beta2; D019951:DNA Polymerase beta; D004259:DNA-Directed DNA Polymerase; C085108:APEX1 protein, human; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase; D000094769:DNA Polymerase iota; C000722070:POLI protein, human
keywords: Apurinic/apyrimidinic endonuclease 1; Base excision repair; Benzo[a]pyrene; Clustered lesions; DNA polymerases