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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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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