Hierarchy of RNA functional dynamics

Annu Rev Biochem. 2014;83:441-66. doi: 10.1146/annurev-biochem-060713-035524. Epub 2014 Mar 5.

Abstract

RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.

Keywords: RNA catalysis; RNA flexibility; molecular adaptation; regulatory RNA; riboswitches.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Base Pairing
  • Genetic Techniques
  • Hydrogen-Ion Concentration
  • Kinetics
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Motion
  • Nucleic Acid Conformation*
  • Protein Conformation
  • Proteins / chemistry
  • RNA / chemistry*
  • Temperature
  • Thermodynamics

Substances

  • Ligands
  • Proteins
  • RNA