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Entropy 2013, 15(8), 3088-3099; doi:10.3390/e15083088

Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers

Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
* Author to whom correspondence should be addressed.
Received: 13 June 2013 / Revised: 15 July 2013 / Accepted: 22 July 2013 / Published: 31 July 2013
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
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To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of thiamine pyrophosphate (TPP) riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific hairpin configuration by the time they have been transcribed, fold with higher efficiency than Shine-Dalgarno sequesterers, whose proper structure is required only at the time of ribosomal binding. Our findings suggest both that riboswitch transcriptional terminator sequences have been naturally selected for high folding efficiency, and that sequesterers can maintain their function even in the presence of significant misfolding.
Keywords: nucleic acids; hairpin; folding; Monte Carlo; kinetic; simulation nucleic acids; hairpin; folding; Monte Carlo; kinetic; simulation
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Sauerwine, B.; Widom, M. Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers. Entropy 2013, 15, 3088-3099.

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