Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels

Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels Full article

Journal

Journal of Physical Chemistry B
ISSN: 1520-6106

Output data

Year: 2016, Volume: 120, Number: 23, Pages: 5125-5133 Pages count : 9 DOI: 10.1021/acs.jpcb.6b03193

Authors

Lomzov Alexander A. ^1,2 , Sviridov Eugeniy A. ^2,3 , Shernuykov Andrey V. ³ , Shevelev Georgiy Yu. ^1,2 , Pyshnyi Dmitrii V. ^1,2 , Bagryanskaya Elena G. ^2,3

Affiliations

1	(Данные Web of science) SB RAS, Inst Chem Biol & Fundamental Med, 8 Lavrentiev Ave, Novosibirsk 630090, Russia
2	(Данные Web of science) Novosibirsk State Univ, Novosibirsk 630090, Russia
3	(Данные Web of science) SB RAS, NN Vorozhtsov Novosibirsk Inst Organ Chem, 9 Lavrentiev Ave, Novosibirsk 630090, Russia

Pulse dipole dipole electron paramagnetic resonance (EPR) spectroscopy (double electron electron resonance [DEER] or pulse electron electron double resonance [PELDOR] and double quantum coherence [DQC]) allows for measurement of distances in biomolecules and can be used at low temperatures in a frozen solution. Recently, the possibility of distance measurement in a nucleic acid at a physiological temperature using pulse EPR was demonstrated: In these experiments, triarylmethyl (TAM) radicals with long memory time of the electron spin served as a spin label. In addition, the duplex was immobilized on modified silica gel particles (Nucleosil DMA); this approach enables measurement of interspin distances close to 4.5 nm. Nevertheless, the possible influence of TAM on the structure of a biopolymer under study and validity of the data obtained by DQC are debated. In this paper, a combination of molecular dynamics (MD) and nuclear magnetic resonance (NMR) methods was used for verification of interspin distances measured by the X-band DQC method. NMR is widely used for structural analysis of biomolecules under natural conditions (room temperature and an aqueous solution). The ultraviolet (UV) melting method and thermal series H-1 NMR in the range 5-95 degrees C revealed the presence of only the DNA duplex in solution at oligonucleotide concentrations 1 mu M to 1.1 mM at temperatures below 40 degrees C. The duplex structures and conformation flexibility of native and TAM-labeled DNA complexes obtained by MD simulation were the same as the structure obtained by NMR refinement. Thus, we showed, that distance measurements at physiological temperatures by the X-band DQC method allow researchers to obtain valid structural information on an unperturbed DNA duplex using terminal TAM spin labels.

Lomzov A.A. , Sviridov E.A. , Shernuykov A.V. , Shevelev G.Y. , Pyshnyi D.V. , Bagryanskaya E.G.
Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels
Journal of Physical Chemistry B. 2016. V.120. N23. P.5125-5133. DOI: 10.1021/acs.jpcb.6b03193 WOS Scopus РИНЦ

Published online:	Jun 3, 2016
Published print:	Jun 16, 2016

Web of science	WOS:000378194900003
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