Folding kinetics of riboswitch transcriptional terminators and sequesterers

DOI10.3390/E15083088zbMATH Open1335.92069arXiv1307.3961OpenAlexW3105775097MaRDI QIDQ280477FDOQ280477

Ben Sauerwine, Michael Widom

Publication date: 10 May 2016

Published in: Entropy (Search for Journal in Brave)

Abstract: 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 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.

Full work available at URL: https://arxiv.org/abs/1307.3961

zbMATH Keywords

Monte Carlosimulationfoldinghairpinkineticnucleic acids

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Monte Carlo methods (65C05) Protein sequences, DNA sequences (92D20)

Cites Work

• Arrhenius lifetimes of RNA structures from free energy landscapes

Cited In (2)

• Determination of hammerhead ribozyme kinetic constants at high molar ratio ribozyme-substrate
• Counting infinitely by oritatami co-transcriptional folding

This page was built for publication: Folding kinetics of riboswitch transcriptional terminators and sequesterers

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q280477)