Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.
Double electron-electron resonance (DEER) was applied to determine nanometre spin-spin distances on DNA duplexes that contain selected structural alterations. The present approach to evaluate the structural features of DNA damages is thus related to the interspin distance changes, as well as to the flexibility of the overall structure deduced from the distance distribution. A set of site-directed nitroxide-labelled double-stranded DNA fragments containing defined lesions, namely an 8-oxoguanine, an abasic site or abasic site analogues, a nick, a gap and a bulge structure were prepared and then analysed by the DEER spectroscopic technique. New insights into the application of 4-pulse DEER sequence are also provided, in particular with respect to the spin probes' positions and the rigidity of selected systems. The lesion-induced conformational changes observed, which were supported by molecular dynamics studies, confirm the results obtained by other, more conventional, spectroscopic techniques. Thus, the experimental approaches described herein provide an efficient method for probing lesion-induced structural changes of nucleic acids.
Sicoli
Giuseppe
G
Laboratoire de Résonance Magnétique, UMR-E no 3 CEA-UJF FRE 3200 CNRS/Institut des Nanosciences et Cryogénie, CEA-Grenoble, 17, Avenue des Martyrs, F-38054, Grenoble Cedex 9, France.
Mathis
Gérald
G
Aci-Sèche
Samia
S
Saint-Pierre
Christine
C
Boulard
Yves
Y
Gasparutto
Didier
D
Gambarelli
Serge
S
D003198:Computer Simulation; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D004249:DNA Damage; D004578:Electron Spin Resonance Spectroscopy; D008958:Models, Molecular; D013113:Spin Labels
D013113:Spin Labels; D004247:DNA