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RNA Structure Prediction: An Overview of Methods

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Bacterial Regulatory RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 905))

Abstract

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.

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Acknowledgments

The authors thank Joseph E. Wedekind for helpful comments. This contribution was supported by the National Institutes of Health grant R01GM076485 to D.H.M.

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Authors and Affiliations

  1. Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY, USA

    Matthew G. Seetin

  2. Department of Biochemistry & Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA

    David H. Mathews

  3. Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY, USA

    David H. Mathews

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Correspondence to David H. Mathews .

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  1. , Dept. of Biochemistry and Molecular Biol, The Pennsylvania State University, Althouse Laboratory 0401, University Park, 16802, USA

    Kenneth C. Keiler

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© 2012 Springer Science+Business Media, LLC

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Seetin, M.G., Mathews, D.H. (2012). RNA Structure Prediction: An Overview of Methods. In: Keiler, K. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 905. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-949-5_8

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  • DOI: https://doi.org/10.1007/978-1-61779-949-5_8

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-948-8

  • Online ISBN: 978-1-61779-949-5

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