2023 PCCP HOT Articles: 19F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

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2023 PCCP HOT Articles

На сайте журнала  Physical Chemistry Chemical Physics,   (IF 3,3) опубликована статья с участием сотрудников Лаборатории магнитной радиоспектроскопии НИОХ:  мнс Н.Б. Асанбаевой, к.х.н., снс О.Ю. Рогожниковой, к.х.н., снсн В.М. Тормышева, к.х.н., снс А.В. Шернюкова, к.х.н., снсн А.М. Генаева и д.ф.-м.н., проф. Е.Г. Багрянской (директор Института)

¹⁹F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

N. B. Asanbaeva, D. S. Novopashina,  O. Yu. Rogozhnikova, V. M. Tormyshev, A. Kehl,  A. A. Sukhanov,  A. V. Shernyukov,  A. M. Genaev, A. A. Lomzov, M. Bennati, A. Meyerde and E. G. Bagryanskaya

Phys. Chem. Chem. Phys., 2023,
First published on 29 Jul 2023

doi: 10.1039/D3CP02969G

Abstract

The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is emerging as a powerful technique for obtaining structural information about proteins and nucleic acids. In this work, we explored the capability of Mims ¹⁹F ENDOR experiments on reporting intermolecular distances in trityl- and ¹⁹F-labeled DNA duplexes at three electron paramagnetic resonance (EPR) frequencies (34, 94, and 263 GHz). For spin labeling, we used the hydrophobic Finland trityl radical and hydrophilic OX063 trityl radical. Fluorine labels were introduced into two positions of a DNA oligonucleotide. The results indicated that hyperfine splittings visible in the ENDOR spectra are consistent with the most populated interspin distances between ¹⁹F and the trityl radical predicted from molecular dynamic (MD) simulations. Moreover, for some cases, ENDOR spectral simulations based on MD results were able to reproduce the conformational distribution reflected in the experimental ENDOR line broadening. Additionally, MD simulations provided more detailed information about the melting of terminal base pairs of the oligonucleotides and about the configuration of the trityls relative to a DNA end.

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