Complementary-addressed site-directed spin labeling of long natural RNAs

Complementary-addressed site-directed spin labeling of long natural RNAs Full article

Journal

Nucleic Acids Research
ISSN: 0305-1048 , E-ISSN: 1362-4962

Output data

Year: 2016, Volume: 44, Number: 16, Pages: 7935-7943 Pages count : 9 DOI: 10.1093/nar/gkw516

Authors

Babaylova Elena S. ^1,2 , Malygin Alexey A. ^1,2 , Lomzov Alexander A. ^1,2 , Pyshnyi Dmitrii V. ^1,2 , Yulikov Maxim ³ , Jeschke Gunnar ³ , Krumkacheva Olesya A. ^2,4 , Fedin Matvey V. ^2,4 , Karpova Galina G. ^1,2 , Bagryanskaya Elena G. ^2,5

Affiliations

1	(Данные Web of science) Inst Chem Biol & Fundamental Med SB RAS, Novosibirsk 630090, Russia
2	(Данные Web of science) Novosibirsk State Univ, Novosibirsk 630090, Russia
3	(Данные Web of science) ETH, Phys Chem Lab, CH-8093 Zurich, Switzerland
4	(Данные Web of science) Int Tomog Ctr SB RAS, Novosibirsk 630090, Russia
5	(Данные Web of science) NN Vorozhtsov Novosibirsk Inst Organ Chem SB RAS, Novosibirsk 630090, Russia

Nanoscale distance measurements by pulse dipolar Electron paramagnetic resonance (EPR) spectroscopy allow new insights into the structure and dynamics of complex biopolymers. EPR detection requires site directed spin labeling (SDSL) of biomolecule(s), which remained challenging for long RNAs up-to-date. Here, we demonstrate that novel complementary-addressed SDSL approach allows efficient spin labeling and following structural EPR studies of long RNAs. We succeeded to spin-label Hepatitis C Virus RNA internal ribosome entry site consisting of a parts per thousand 330 nucleotides and having a complicated spatial structure. Application of pulsed double electron-electron resonance provided spin-spin distance distribution, which agrees well with the results of molecular dynamics (MD) calculations. Thus, novel SDSL approach in conjunction with EPR and MD allows structural studies of long natural RNAs with nanometer resolution and can be applied to systems of biological and biomedical significance.

Babaylova E.S. , Malygin A.A. , Lomzov A.A. , Pyshnyi D.V. , Yulikov M. , Jeschke G. , Krumkacheva O.A. , Fedin M.V. , Karpova G.G. , Bagryanskaya E.G.
Complementary-addressed site-directed spin labeling of long natural RNAs

Nucleic Acids Research. 2016. V.44. N16. P.7935-7943. DOI: 10.1093/nar/gkw516 WOS Scopus РИНЦ

Full text from publisher

Published online:	Jun 6, 2016
Published print:	Sep 19, 2016

Web of science	WOS:000384687000037
Scopus	2-s2.0-84988934376
Elibrary	27569813
OpenAlex	W2418895284