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Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.

ABSTRACT: 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.

SUBMITTER: Sicoli G

PROVIDER: S-EPMC2691821 | biostudies-other | 2009 Jun

REPOSITORIES: biostudies-other

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Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.

Sicoli Giuseppe G Mathis Gérald G Aci-Sèche Samia S Saint-Pierre Christine C Boulard Yves Y Gasparutto Didier D Gambarelli Serge S

Nucleic acids research 20090320 10

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, ...[more]

PMID: 19304747

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Project description:Q-band and X-band pulsed electron paramagnetic resonance spectroscopic methods (EPR) in the solid state were employed to refine the parameters characterizing the anisotropic interactions present in six nitroxide radicals prepared by N,N addition of NO to various borane-phosphane frustrated Lewis pairs (FLPs). The EPR spectra are characterized by the g-anisotropy as well as by nuclear hyperfine coupling between the unpaired electron and the 11B/10B, 14N and 31P nuclear magnetic moments. It was previously shown that continuous-wave spectra measured at X-band frequency (9.5 GHz) are dominated by the magnetic hyperfine coupling to 14N and 31P, whereas the g-tensor values and the 11B hyperfine coupling parameters cannot be refined with high precision from lineshape fitting. On the other hand, the X-band electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) spectra are completely dominated by the nuclear hyperfine coupling to the 11B nuclei, allowing a selective determination of their interaction parameters. In the present work this analysis has been further validated by temperature dependent ESEEM measurements. In addition, pulsed EPR data measured in the Q-band (34 GHz) are reported, which present an entirely different situation: the g-tensor components can be measured with much higher precision, and the ESEEM and HYSCORE spectra contain information about all of the 10B, 11B, 14N and 31P hyperfine interaction parameters. Based on these new results, we report here high-accuracy and precision data of the EPR spin Hamiltonian parameters measured on six FLP-NO radical species embedded in their corresponding hydroxylamine host structures. While the ESEEM spectra at Q-band frequency turn out to be very complex (due to the multinuclear contribution to the overall signal) in the HYSCORE experiment the extension over two dimensions renders a better discrimination between the different nuclear species, and the signals arising from hyperfine coupling to 10B, 11B, 14N and 31P nuclei can be individually analyzed.

Dataset Information

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.

Publications

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling.

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