Efficient computation of co-transcriptional RNA-ligand interaction dynamics

Methods. 2018 Jul 1;143:70-76. doi: 10.1016/j.ymeth.2018.04.036. Epub 2018 May 4.


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.

Keywords: Co-transcriptional folding; Energy landscape; RNA dynamics; RNA-ligand interaction; Riboswitch.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics
  • Computational Biology / methods*
  • Entomoplasmataceae / genetics
  • Kinetics
  • Ligands
  • Models, Biological
  • Nucleic Acid Conformation*
  • RNA Folding
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / metabolism
  • Riboswitch / genetics*
  • Transcription, Genetic*


  • Ligands
  • RNA, Bacterial
  • Riboswitch