Encyclopedia of Biophysics

2013 Edition
| Editors: Gordon C. K. Roberts

Modeling of RNA Molecules

  • David Dufour
  • Marc A. Marti-Renom
Reference work entry
DOI: https://doi.org/10.1007/978-3-642-16712-6_154

Synonyms

 RNA

Definition

Modeling of Ribo-Nucleic Acid (RNA) molecules is the determination/prediction of secondary and tertiary RNA structures by using experimental or theoretical approaches.

Introduction

Until recently, RNA has been considered a transfer molecule in the genetic information flow process. However, the myriad of noncoding RNAs recently discovered has shown a plethora of new functions that are now attributed to it. These functions include among others biological catalysis (e.g., ribozymes), gene regulation (e.g., micro-RNAs), or host defense (e.g., small interfering RNAs). Knowledge of the secondary and tertiary structures of such RNA molecules will provide insights on the molecular mechanisms of their diverse functions. X-Ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and single-particle electron microscopy are the main biophysical techniques used for determining RNA secondary and/or tertiary structures. Moreover, theoretical approaches are now...

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References

  1. Capriotti E, Marti-Renom MA. Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC Bioinformatics. 2010;11:322.PubMedCentralPubMedGoogle Scholar
  2. Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA. 2001;7:499–512.PubMedGoogle Scholar
  3. Mathews DH, Turner DH. Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol. 2006;16:270–8.PubMedGoogle Scholar
  4. Mathews DH, Moss WN, Turner DH. Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol. 2010;2:a003665.PubMedGoogle Scholar
  5. Moore PB. Structural motifs in RNA. Annu Rev Biochem. 1999;68:287–300.PubMedGoogle Scholar
  6. Neidle S, Schneider B, Berman HM. Fundamentals of DNA and RNA structure. In: Bourne PE, Gu J, editors. Structural bioinformatics. 2nd ed. Hoboken: Wiley-Blackwell; 2009. p. 41–76.Google Scholar
  7. Shapiro BA, Yingling YG, Kasprzak W, Bindewald E. Bridging the gap in RNA structure prediction. Curr Opin Struct Biol. 2007;17:157–65.PubMedGoogle Scholar

Copyright information

© European Biophysical Societies' Association (EBSA) 2013

Authors and Affiliations

  1. 1.Structural Genomics GroupNational Center for Genomic Analysis (CNAG)BarcelonaSpain