Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

J Am Chem Soc. 2012 Feb 8;134(5):2800-6. doi: 10.1021/ja211328g. Epub 2012 Jan 27.

Abstract

Canonical duplex RNA assumes only the A-form conformation at the secondary structure level while, in contrast, a wide range of noncanonical, tertiary conformations of RNA occur. Here, we show how the 2'-hydroxyl controls RNA conformational properties. Quantum mechanical calculations reveal that the orientation of the 2'-hydroxyl significantly alters the intrinsic flexibility of the phosphodiester backbone, favoring the A-form in duplex RNA when it is in the base orientation and facilitating sampling of a wide range of noncanonical, tertiary structures when it is in the O3' orientation. Influencing the orientation of the 2'-hydroxyl are interactions with the environment, as evidenced by crystallographic survey data, indicating the 2'-hydroxyl to sample more of the O3' orientation in noncanonical RNA structures. These results indicate that the 2'-hydroxyl acts as a "switch", both limiting the conformation of RNA to the A-form at the secondary structure level and allowing RNA to sample a wide range of noncanonical tertiary conformations.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA / chemistry
  • Hydroxides / chemistry*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Quantum Theory
  • RNA / chemistry*

Substances

  • Hydroxides
  • RNA
  • DNA
  • hydroxide ion