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Int. J. Mol. Sci. 2017, 18(11), 2442; https://doi.org/10.3390/ijms18112442

Computational Methods for Modeling Aptamers and Designing Riboswitches

1
Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang 438000, China
2
Department of Physics, Wuhan University, Wuhan 430072, China
*
Author to whom correspondence should be addressed.
Received: 19 October 2017 / Revised: 12 November 2017 / Accepted: 14 November 2017 / Published: 17 November 2017
(This article belongs to the Special Issue Aptamers)
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Abstract

Riboswitches, which are located within certain noncoding RNA region perform functions as genetic “switches”, regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers. As structural changes in aptamers must be achieved within the certain time window for effective regulation, kinetics is another key point for understanding aptamer function in riboswitch-mediated gene regulation. The coarse-grained self-organized polymer (SOP) model using Langevin dynamics simulation has been successfully developed to investigate folding kinetics of aptamers, while their co-transcriptional folding kinetics can be modeled by the helix-based computational method and BarMap approach. Based on the known aptamers, the web server Riboswitch Calculator and other theoretical methods provide a new tool to design synthetic riboswitches. This review will represent an overview of these computational methods for modeling structure and kinetics of riboswitch aptamers and for designing riboswitches. View Full-Text
Keywords: riboswitch; aptamer; mRNA structure; gene regulation riboswitch; aptamer; mRNA structure; gene regulation
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Gong, S.; Wang, Y.; Wang, Z.; Zhang, W. Computational Methods for Modeling Aptamers and Designing Riboswitches. Int. J. Mol. Sci. 2017, 18, 2442.

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