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Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules

Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion–RNA and ligand–RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data–directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Annual Review of Biophysics Annual Reviews

Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules

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Publisher
Annual Reviews
Copyright
Copyright © 2017 by Annual Reviews. All rights reserved
ISSN
1936-122X
eISSN
1936-1238
DOI
10.1146/annurev-biophys-070816-033920
pmid
28301768
Publisher site
See Article on Publisher Site

Abstract

In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion–RNA and ligand–RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data–directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model.

Journal

Annual Review of BiophysicsAnnual Reviews

Published: May 22, 2017

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