title: PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes.
abstract: PELDOR (pulsed electron-electron double resonance) spectroscopy was applied to determine spin-spin distances in spin-labeled DNA duplexes (13-mer and 17-mer) containing the damaged sites 8-oxoguanine or uncleavable abasic site analogue tetrahydrofuran. The lesions were located in one strand of the DNA, and two nitroxyl spin labels were attached at the 5'- and 3'-ends of the complementary strand. PELDOR data allow us to obtain distances between the two spin labels in DNAs, which turned out to be around 5 nm for the 13-mer DNA and around 6 nm for 17-mer DNA. Results of PELDOR measurements were supported by molecular dynamics calculations. Study of the interaction of DNA fragments with DNA repair enzyme 8-oxoguanine-DNA glycosylase from E. coli (Fpg protein) showed that this interaction leads to a noticeable decrease of the distance between spin labels, which indicates the enzyme-induced bending of the DNA duplex. This bending may be important for the mechanisms of recognition of damaged sites by DNA repair enzymes.
authors: Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Lavrentyev Ave. 8, 630090, Novosibirsk, Russia.
authors: N A
authors: NA
authors: Kuznetsov
authors: A D
authors: AD
authors: Milov
authors: N P
authors: NP
authors: Isaev
authors: Yu N
authors: YN
authors: Vorobjev
authors: V V
authors: VV
authors: Koval
authors: S A
authors: SA
authors: Dzuba
authors: O S
authors: OS
authors: Fedorova
authors: Yu D
authors: YD
authors: Tsvetkov
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D015394:Molecular Structure
chemical_list: D004247:DNA