TY - JOUR

T1 - Processing of the abasic sites clustered with the benzo[a]pyrene adducts by the base excision repair enzymes

AU - Starostenko, Lidia V.

AU - Rechkunova, Nadejda I.

AU - Lebedeva, Natalia A.

AU - Lomzov, Alexander A.

AU - Koval, Vladimir V.

AU - Lavrik, Olga I.

N1 - Copyright © 2016 Elsevier B.V. All rights reserved.

PY - 2017/2/1

Y1 - 2017/2/1

N2 - 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.

AB - 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.

KW - Apurinic/apyrimidinic endonuclease 1

KW - Base excision repair

KW - Benzo[a]pyrene

KW - Clustered lesions

KW - DNA polymerases

KW - DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism

KW - Catalytic Domain

KW - DNA Polymerase beta/metabolism

KW - Humans

KW - 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/metabolism

KW - Molecular Dynamics Simulation

KW - DNA Repair

KW - Protein Conformation

KW - DNA Damage

KW - Nucleic Acid Conformation

KW - DNA-Directed DNA Polymerase

KW - DNA Adducts/metabolism

KW - INCISION ACTIVITY

KW - EXONUCLEASE ACTIVITY

KW - HUMAN APURINIC ENDONUCLEASE

KW - CATALYTIC MECHANISM

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - HUMAN AP ENDONUCLEASE

KW - SOLUTION CONFORMATION

KW - LYASE ACTIVITY

KW - DNA-POLYMERASE-LAMBDA

KW - HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE

UR - http://www.scopus.com/inward/record.url?scp=85008331107&partnerID=8YFLogxK

U2 - 10.1016/j.dnarep.2016.12.007

DO - 10.1016/j.dnarep.2016.12.007

M3 - Article

C2 - 28065385

AN - SCOPUS:85008331107

VL - 50

SP - 43

EP - 53

JO - DNA Repair

JF - DNA Repair

SN - 1568-7864

ER -