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Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.

Publication ,  Journal Article
Clay, MC; Ganser, LR; Merriman, DK; Al-Hashimi, HM
Published in: Nucleic Acids Res
August 21, 2017

Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.

Duke Scholars

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

August 21, 2017

Volume

45

Issue

14

Start / End Page

e134

Location

England

Related Subject Headings

  • Thermodynamics
  • RNA, Viral
  • RNA
  • Nucleic Acid Conformation
  • Nitrogen Isotopes
  • Mutation
  • Magnetic Resonance Spectroscopy
  • HIV-1
  • Developmental Biology
  • Carbon Isotopes
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Clay, M. C., Ganser, L. R., Merriman, D. K., & Al-Hashimi, H. M. (2017). Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res, 45(14), e134. https://doi.org/10.1093/nar/gkx525
Clay, Mary C., Laura R. Ganser, Dawn K. Merriman, and Hashim M. Al-Hashimi. “Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic Acids Res 45, no. 14 (August 21, 2017): e134. https://doi.org/10.1093/nar/gkx525.
Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res. 2017 Aug 21;45(14):e134.
Clay, Mary C., et al. “Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic Acids Res, vol. 45, no. 14, Aug. 2017, p. e134. Pubmed, doi:10.1093/nar/gkx525.
Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res. 2017 Aug 21;45(14):e134.
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

August 21, 2017

Volume

45

Issue

14

Start / End Page

e134

Location

England

Related Subject Headings

  • Thermodynamics
  • RNA, Viral
  • RNA
  • Nucleic Acid Conformation
  • Nitrogen Isotopes
  • Mutation
  • Magnetic Resonance Spectroscopy
  • HIV-1
  • Developmental Biology
  • Carbon Isotopes