Michael T. Wolfinger

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Jul 01 2018 Efficient Computation of Cotranscriptional RNA-Ligand Interaction Dynamics

Co-transcriptional RNA-ligand interaction dynamics are simulated for riboswitches under kinetic control

Abstract

Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2′-deoxyguanosine (2′dG)-sensing riboswitch from Mesoplasma florum.

Reference

Efficient Computation of Cotranscriptional RNA-Ligand Interaction Dynamics
Michael T. Wolfinger, Christoph Flamm, Ivo L. Hofacker
Methods 143:70–76 (2018) | doi: 10.1016/j.ymeth.2018.04.036 | PDF

Citations

Posted by Michael T. Wolfinger on Sun 01 July 2018. updated Tue 15 February 2022

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