title: 8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme.
abstract: 8-oxoguanine is one of the most abundant and impactful oxidative DNA lesions. However, the reasons underlying its effects, especially those not directly explained by the altered base pairing ability, are poorly understood. We report the effect of the lesion on the action of EcoRI, a widely used restriction endonuclease. Introduction of 8-oxoguanine inside, or adjacent to, the GAATTC recognition site embedded within the Drew-Dickerson dodecamer sequence notably reduced the EcoRI activity. Solution NMR revealed that 8-oxoguanine in the DNA duplex causes substantial alterations in the sugar-phosphate backbone conformation, inducing a BI→BII transition. Moreover, molecular dynamics of the complex suggested that 8-oxoguanine, although does not disrupt the sequence-specific contacts formed by the enzyme with DNA, shifts the distribution of BI/BII backbone conformers. Based on our data, we propose that the disruption of enzymatic cleavage can be linked with the altered backbone conformation and dynamics in the free oxidized DNA substrate and, possibly, at the protein-DNA interface.
authors.affiliation: Chemistry Department, Western Washington University, Bellingham, WA, United States of America.
authors.forename: Joanna J
authors.initials: JJ
authors.lastname: Hoppins
authors.affiliation: Chemistry Department, Western Washington University, Bellingham, WA, United States of America.
authors.forename: David R
authors.initials: DR
authors.lastname: Gruber
authors.affiliation: Chemistry Department, Western Washington University, Bellingham, WA, United States of America.
authors.forename: Heather L
authors.initials: HL
authors.lastname: Miears
authors.affiliation: SB RAS International Tomography Center, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kiryutin
authors.affiliation: SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.|Institute of Biochemistry, Stuttgart University, Stuttgart, Germany.
authors.forename: Rustem D
authors.initials: RD
authors.lastname: Kasymov
authors.affiliation: Novosibirsk State University, Novosibirsk, Russia.|SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
authors.forename: Darya V
authors.initials: DV
authors.lastname: Petrova
authors.affiliation: Novosibirsk State University, Novosibirsk, Russia.|SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
authors.forename: Anton V
authors.initials: AV
authors.lastname: Endutkin
authors.affiliation: SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Popov
authors.affiliation: SB RAS International Tomography Center, Novosibirsk, Russia.|Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Alexandra V
authors.initials: AV
authors.lastname: Yurkovskaya
authors.affiliation: Chemistry Department, Western Washington University, Bellingham, WA, United States of America.|University of California Santa Cruz, Program in Biomedical Science and Engineering, Santa Cruz, CA, United States of America.
authors.forename: Stanislav O
authors.initials: SO
authors.lastname: Fedechkin
authors.affiliation: Chemistry Department, Western Washington University, Bellingham, WA, United States of America.|Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Jacob A
authors.initials: JA
authors.lastname: Brockerman
authors.affiliation: Novosibirsk State University, Novosibirsk, Russia.|SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
authors.forename: Dmitry O
authors.initials: DO
authors.lastname: Zharkov
authors.affiliation: Chemistry Department, Western Washington University, Bellingham, WA, United States of America.
authors.forename: Serge L
authors.initials: SL
authors.lastname: Smirnov
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D053837:DNA Cleavage; D004249:DNA Damage; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism*; D006147:Guanine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
chemical_list: C024829:8-hydroxyguanine; D006147:Guanine; D004247:DNA; D015246:Deoxyribonuclease EcoRI