Triarylmethyl Labels: Toward Improving the Accuracy of EPR Nanoscale Distance Measurements in DNAs

Triarylmethyl Labels: Toward Improving the Accuracy of EPR Nanoscale Distance Measurements in DNAs Full article

Journal

Journal of Physical Chemistry B
ISSN: 1520-6106

Output data

Year: 2015, Volume: 119, Number: 43, Pages: 13641-13648 Pages count : 8 DOI: 10.1021/acs.jpcb.5b03026

Authors

Shevelev Georgiy Yu. ^1,4 , Krumkacheva Olesya A. ⁴ , Lomzov Alexander A. ^1,4 , Kuzhelev Andrey A. ^3,4 , Trukhin Dmitry V. ^3,4 , Rogozhnikova Olga Yu. ^3,4 , Tormyshev Victor M. ^3,4 , Pyshnyi Dmitrii V. ^1,4 , Fedin Matvey V. ^2,4 , Bagryanskaya Elena G. ^3,4

Affiliations

1	(Данные Web of science) RAS, SB, Inst Chem Biol & Fundamental Med, Novosibirsk 630090, Russia
2	(Данные Web of science) RAS, SB, Int Tomog Ctr, Novosibirsk 630090, Russia
3	(Данные Web of science) RAS, SB, NN Vorozhtsov Novosibirsk Inst Organ Chem, Novosibirsk 630090, Russia
4	(Данные Web of science) Novosibirsk State Univ, Novosibirsk 630090, Russia

Triarylmethyl (trityl, TAM) based spin labels represent a promising alternative to nitroxides for EPR distance measurements in biomolecules. Herewith, we report synthesis and comparative study of series of model DNA duplexes, 5'-spin-labeled with TAMs and nitroxides. We have found that the accuracy (width) of distance distributions obtained by double electron electron resonance (DEER/PELDOR) strongly depends on the type of radical. Replacement of both nitroxides by TAMs in the same spin-labeled duplex allows narrowing of the distance distributions by a factor of 3. Replacement of one nitroxide by TAM (orthogonal labeling) leads to a less pronounced narrowing but at the same time gains sensitivity in DEER experiment due to efficient pumping on the narrow EPR line of TAM. Distance distributions in nitroxide/nitroxide pairs are influenced by the structure of the linker: the use of a short amine-based linker improves the accuracy by a factor of 2. At the same time, a negligible dependence on the linker length is found for the distribution width in TAM/TAM pairs. Molecular dynamics calculations indicate greater conformational disorder of nitroxide labels compared to TAM ones, thus rationalizing the experimentally observed trends. Thereby, we conclude that double spin-labeling using TAMs allows obtaining narrower spin-spin distance distributions and potentially more precise distances between labeling sites compared to traditional nitroxides.

Shevelev G.Y. , Krumkacheva O.A. , Lomzov A.A. , Kuzhelev A.A. , Trukhin D.V. , Rogozhnikova O.Y. , Tormyshev V.M. , Pyshnyi D.V. , Fedin M.V. , Bagryanskaya E.G.
Triarylmethyl Labels: Toward Improving the Accuracy of EPR Nanoscale Distance Measurements in DNAs

Journal of Physical Chemistry B. 2015. V.119. N43. P.13641-13648. DOI: 10.1021/acs.jpcb.5b03026 WOS Scopus РИНЦ

Full text from publisher

Published online:	Jun 4, 2015
Published print:	Oct 29, 2015

Web of science	WOS:000363994000019
Scopus	2-s2.0-84946071683
Elibrary	24968406
OpenAlex	W2413369001