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RNA Tertiary Structure

Nucleic Acids Structure and Mapping

  1. Eric Westhof,
  2. Pascal Auffinger

Published Online: 15 SEP 2006

DOI: 10.1002/9780470027318.a1428

Encyclopedia of Analytical Chemistry

Encyclopedia of Analytical Chemistry

How to Cite

Westhof, E. and Auffinger, P. 2006. RNA Tertiary Structure. Encyclopedia of Analytical Chemistry. .

Author Information

  1. Institute of Molecular and Cellular Biology, Strasbourg, France

Publication History

  1. Published Online: 15 SEP 2006

Abstract

Ribonucleic acids are negatively charged polymers assembled from four different types of monomers. Each monomer is made of an invariant phosphorylated sugar to which is attached one of the four standard nucleic acid bases; the pyrimidines uracil and cytosine, and the purines guanine and adenine. The first level of organization is thus the sequence of bases attached to the sugar–phosphate backbone. In salty water, the RNA molecules fold back on themselves via Watson–Crick base pairing between the bases (A with U, G with C or U) leading to double-stranded helices interrupted by single-stranded regions in internal loops or hairpin loops. The enumeration of the base-paired regions or helices constitutes a description of the second level of organization, the secondary structure. The methods available to deduce the secondary structure of an RNA molecule are mainly of three types: the phylogenetic approach, the theoretical prediction, and chemical/enzymatic methods. The secondary structure of an RNA molecule is experimentally accessible and its content measurable. Under appropriate conditions, structured RNA molecules undergo a transition to a three-dimensional (3D) fold in which the helices and the unpaired regions are precisely organized in space. This folding process usually depends on the presence of divalent ions, such as magnesium ions, and on the temperature. The tertiary structure is the level of organization relevant for biological function of structured RNA molecules.