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A New Method to Predict Ion Effects in RNA Folding

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RNA Nanostructures

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1632))

Abstract

The strong interaction between metal ions in solution and highly charged RNA molecules is critical for RNA structure formation and stabilization. Metal ions binding to RNA can induce RNA structural changes that are important for RNA cellular functions. Therefore, quantitative modeling of the ion effects is essential for RNA structure prediction and RNA-based molecular design. Recently, inspired by the increasing experimental evidence that supports the importance of ion correlation and fluctuation in ion–RNA interactions, we developed a new computational model, Monte Carlo Tightly Bound Ion (MCTBI) model. The validity of the model is shown by the improved accuracy in the predictions for ion binding properties and ion-dependent free energies for RNA structures. In this chapter, using homodimeric tetraloop-receptor docking as an illustrative example, we showcase the MCTBI method for the computational prediction of the ion effects in RNA folding.

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Acknowledgements

This research was supported by NIH grant GM063732.

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Authors and Affiliations

  1. Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA

    Li-Zhen Sun & Shi-Jie Chen

Authors
  1. Li-Zhen Sun
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  2. Shi-Jie Chen
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Correspondence to Shi-Jie Chen .

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Editors and Affiliations

  1. Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland, USA

    Eckart Bindewald

  2. RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA

    Bruce A. Shapiro

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Sun, LZ., Chen, SJ. (2017). A New Method to Predict Ion Effects in RNA Folding. In: Bindewald, E., Shapiro, B. (eds) RNA Nanostructures . Methods in Molecular Biology, vol 1632. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7138-1_1

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  • DOI: https://doi.org/10.1007/978-1-4939-7138-1_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7137-4

  • Online ISBN: 978-1-4939-7138-1

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