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

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-d...

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Bibliographic Details
Published in:Nucleic acids research 2016-09, Vol.44 (16), p.7935-7943
Main Authors: Babaylova, Elena S, Malygin, Alexey A, Lomzov, Alexander A, Pyshnyi, Dmitrii V, Yulikov, Maxim, Jeschke, Gunnar, Krumkacheva, Olesya A, Fedin, Matvey V, Karpova, Galina G, Bagryanskaya, Elena G
Format: Article
Language:English
Subjects:
Alkylation
Base Sequence
Electron Spin Resonance Spectroscopy
Hepacivirus - genetics
Internal Ribosome Entry Sites
Nucleic Acid Conformation
Oligodeoxyribonucleotides - metabolism
RNA
RNA, Viral - chemistry
RNA, Viral - genetics
RNA, Viral - metabolism
Spin Labels
Temperature
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Summary: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 ≈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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkw516