A versatile approach for site-directed spin labeling and structural EPR studies of RNAs

• DOI: 10.1039/c3ob42154f
• Publication Date: 2014-03-11T16:01:05Z
• Authors: Elena S. Babaylova; Anton V. Ivanov; Alexey A. Malygin; Maria A. Vorobjeva; Alia G. Venyaminova; Yuliya F. Polienko; Igor A. Kirilyuk; Olesya A. Krumkac...; Matvey V. Fedin; Galina G. Karpova; Elena G. Bagryans...
• Keywords: Site-directed spin labeling; Linker; Pulsed EPR; Spin label; Duplex (building)

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