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The Determination of RNA Folding Nearest Neighbor Parameters

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RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1097))

Abstract

The stability of RNA secondary structure can be predicted using a set of nearest neighbor parameters. These parameters are widely used by algorithms that predict secondary structure. This contribution introduces the UV optical melting experiments that are used to determine the folding stability of short RNA strands. It explains how the nearest neighbor parameters are chosen and how the values are fit to the data. A sample nearest neighbor calculation is provided. The contribution concludes with new methods that use the database of sequences with known structures to determine parameter values.

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Acknowledgments

The authors thank Jonathan Chen for preparing Figs. 3.1 and 3.2 and Matthew Seetin for helpful comments. The chapter was supported by National Institutes of Health grants R01GM22939 to D.H.T., R01GM076485 to D.H.M., and a grant from the Natural Sciences and Engineering Research Council of Canada to A.C.

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Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA

    David H. Mathews

  2. Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA

    David H. Mathews

  3. Department of Genome Sciences, University of Washington, Seattle, WA, USA

    Mirela Andronescu

  4. Department of Computer Science, University of British Columbia, Vancouver, BC, Canada

    Anne Condon

  5. Department of Chemistry, The College of Arts and Sciences, Rochester, NY, USA

    Douglas H. Turner

Authors
  1. Mirela Andronescu
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  2. Anne Condon
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  3. Douglas H. Turner
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  4. David H. Mathews
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Corresponding author

Correspondence to David H. Mathews .

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Editors and Affiliations

  1. Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

    Jan Gorodkin

  2. University of Washington Dept. Computer Science & Engineering, Seattle, Washington, USA

    Walter L. Ruzzo

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Andronescu, M., Condon, A., Turner, D.H., Mathews, D.H. (2014). The Determination of RNA Folding Nearest Neighbor Parameters. In: Gorodkin, J., Ruzzo, W. (eds) RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Methods in Molecular Biology, vol 1097. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-709-9_3

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  • DOI: https://doi.org/10.1007/978-1-62703-709-9_3

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