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Crumple: An Efficient Tool to Explore Thoroughly the RNA Folding Landscape

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RNA Structure Determination

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1490))

Abstract

The folding landscape for an RNA sequence contains many diverse structures and motifs, which are often sampled rather than completely explored. Today’s supercomputers make the complete enumeration of all possible folds for an RNA and a detailed description of the RNA folding landscape a more feasible task. This chapter provides protocols for using the Crumple folding algorithm, an efficient tool to generate all possible non-pseudoknotted folds for an RNA sequence. Crumple in conjunction with Sliding Windows and Assembly can incorporate experimental constraints on the global features of an RNA, such as the minimum number and lengths of helices, which may be determined by crystallography or cryo-electron microscopy. This complete enumeration method is independent of free-energy minimization and allows the user to incorporate experimental data such as chemical probing, SELEX data on RNA–protein binding motifs, and phylogenetic covariation.

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Acknowledgements

The authors would like to thank Jonathan W. Stone, Samuel Bleckley, and Jui-wen Liu for the development of the Crumple algorithm and RNA folding software in the Schroeder lab. We thank Kimberly Ughamadu for helpful comments on this manuscript and Fig. 8 pilegrams. We thank Henry Neeman and the staff at the Oklahoma Supercomputing Center for Education and Research (OSCER) for advice, assistance, and access to the Sooner and Boomer supercomputers. This work was supported by NSF CAREER award 0844913.

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Authors and Affiliations

  1. Department of Chemistry & Biochemistry, Department of Microbiology &Plant Biology, University ofOklahoma, Norman, OK, USA

    Ivan Guerra & Susan J. Schroeder

Authors
  1. Ivan Guerra
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  2. Susan J. Schroeder
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Corresponding author

Correspondence to Susan J. Schroeder .

Editor information

Editors and Affiliations

  1. Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, New York, USA

    Douglas H. Turner

  2. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA

    David H. Mathews

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Guerra, I., Schroeder, S.J. (2016). Crumple: An Efficient Tool to Explore Thoroughly the RNA Folding Landscape. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Molecular Biology, vol 1490. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6433-8_1

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  • DOI: https://doi.org/10.1007/978-1-4939-6433-8_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6431-4

  • Online ISBN: 978-1-4939-6433-8

  • eBook Packages: Springer Protocols

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