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Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.

Publication ,  Journal Article
Eichhorn, CD; Feng, J; Suddala, KC; Walter, NG; Brooks, CL; Al-Hashimi, HM
Published in: Nucleic Acids Res
February 2012

Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an A-form-like conformation, with the level of order decreasing toward the terminal ends. An A-to-C mutation within the polyadenine tract alters the observed dynamics consistent with the introduction of a dynamic kink. Pre-ordering of the tail may increase the efficacy of ligand binding above that achieved by a random-coil ssRNA. The REMD simulations recapitulate important trends in the NMR data, but suggest more internal motions than inferred from the NMR analysis. Our study unmasks a previously unappreciated level of complexity in ssRNA, which we believe will also serve as an excellent model system for testing and developing computational force fields.

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Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

February 2012

Volume

40

Issue

3

Start / End Page

1345 / 1355

Location

England

Related Subject Headings

  • Riboswitch
  • RNA Stability
  • RNA
  • Pyrroles
  • Pyrimidinones
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • Mutation
  • Molecular Dynamics Simulation
  • Ligands
 

Citation

APA
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ICMJE
MLA
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Eichhorn, C. D., Feng, J., Suddala, K. C., Walter, N. G., Brooks, C. L., & Al-Hashimi, H. M. (2012). Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res, 40(3), 1345–1355. https://doi.org/10.1093/nar/gkr833
Eichhorn, Catherine D., Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks, and Hashim M. Al-Hashimi. “Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.Nucleic Acids Res 40, no. 3 (February 2012): 1345–55. https://doi.org/10.1093/nar/gkr833.
Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL, Al-Hashimi HM. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res. 2012 Feb;40(3):1345–55.
Eichhorn, Catherine D., et al. “Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.Nucleic Acids Res, vol. 40, no. 3, Feb. 2012, pp. 1345–55. Pubmed, doi:10.1093/nar/gkr833.
Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL, Al-Hashimi HM. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res. 2012 Feb;40(3):1345–1355.
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

February 2012

Volume

40

Issue

3

Start / End Page

1345 / 1355

Location

England

Related Subject Headings

  • Riboswitch
  • RNA Stability
  • RNA
  • Pyrroles
  • Pyrimidinones
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • Mutation
  • Molecular Dynamics Simulation
  • Ligands