Abstract: Site-directed spin labeling (SDSL) is widely applied for structural studies of biopolymers by electron paramagnetic resonance (EPR). However, SDSL of long RNA sequences still remains a challenging task. Here, we propose a novel SDSL approach potentially suitable for long natural RNAs, which is based on the attachment of a linker containing an aliphatic amino group to the target nucleotide residue followed by selective coupling of a spin label to this amino group. Such a linker can be attached to the desired RNA residue via a sequence-specific reaction with the derivatives of oligodeoxyribonucleotides. To verify this approach, we applied it to model RNA duplex with known structure and expected distance between corresponding residues. A new 2,5-bis(spirocyclohexane)-substituted spin label with advanced stability and relaxation properties has been used, and the distance distribution measured using Q-band (34 GHz) pulsed double electron-electron resonance corresponds well to the expected one. We have additionally validated the obtained results by studying a similar RNA duplex, where the linker with the aliphatic amino group was introduced via solid-phase synthesis. Although this novel SDSL approach does not provide an advantage in precision of molecular distance measurements, we believe that its applicability to long RNAs is a crucial benefit for future structural studies using pulse EPR.

Cite: Babaylova E.S. , Ivanov A.V. , Malygin A.A. , Vorobjeva M.A. , Venyaminova A.G. , Polienko Y.F. , Kirilyuk I.A. , Krumkacheva O.A. , Fedin M.V. , Karpova G.G. , Bagryanskaya E.G.
A versatile approach for site-directed spin labeling and structural EPR studies of RNAs
Organic and Biomolecular Chemistry. 2014. V.12. N19. P.3129-3136. DOI: 10.1039/c3ob42154f WOS Scopus РИНЦ

Identifiers:

Web of science	WOS:000334924700018
Scopus	2-s2.0-84898807837
Elibrary	21872808
OpenAlex	W2061421884

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