Bacterial Regulatory RNA

Volume 905 of the series Methods in Molecular Biology pp 99-122


RNA Structure Prediction: An Overview of Methods

  • Matthew G. SeetinAffiliated withDepartment of Biochemistry & Biophysics, University of Rochester Medical Center
  • , David H. MathewsAffiliated withDepartment of Biochemistry & Biophysics, Center for RNA Biology, University of Rochester Medical CenterDepartment of Biostatistics & Computational Biology, University of Rochester Medical Center Email author 

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RNA is now appreciated to serve numerous cellular roles, and understanding RNA structure is important for understanding a mechanism of action. This contribution discusses the methods available for predicting RNA structure. Secondary structure is the set of the canonical base pairs, and secondary structure can be accurately determined by comparative sequence analysis. Secondary structure can also be predicted. The most commonly used method is free energy minimization. The accuracy of structure prediction is improved either by using experimental mapping data or by predicting a structure conserved in a set of homologous sequences. Additionally, tertiary structure, the three-dimensional arrangement of atoms, can be modeled with guidance from comparative analysis and experimental techniques. New approaches are also available for predicting tertiary structure.

Key words

Statistical mechanics Comparative sequence analysis Gibbs free energy Dynamic programming algorithm RNA secondary structure