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

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Clay, MC; Ganser, LR; Merriman, DK; Al-Hashimi, HM

Published Date

  • August 21, 2017

Published In

Volume / Issue

  • 45 / 14

Start / End Page

  • e134 -

PubMed ID

  • 28609788

Pubmed Central ID

  • 28609788

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

Digital Object Identifier (DOI)

  • 10.1093/nar/gkx525

Language

  • eng

Conference Location

  • England