Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

Mol Cell. 2021 Feb 18;81(4):870-883.e10. doi: 10.1016/j.molcel.2020.12.017. Epub 2021 Jan 15.


The series of RNA folding events that occur during transcription can critically influence cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a method to uncover details of cotranscriptional RNA folding. We model the folding of the Escherichia coli signal recognition particle (SRP) RNA and show that it requires specific local structural fluctuations within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the functional structure. All-atom molecular dynamics simulations suggest that this rearrangement proceeds through an internal toehold-mediated strand-displacement mechanism, which can be disrupted with a point mutation that limits local structural fluctuations and rescued with compensating mutations that restore these fluctuations. Moreover, a cotranscriptional folding intermediate could be cleaved in vitro by recombinant E. coli RNase P, suggesting potential cotranscriptional processing. These results from experiment-guided multi-scale modeling demonstrate that even an RNA with a simple functional structure can undergo complex folding and processing during synthesis.

Keywords: RNA; RNA fluctuations; RNA folding dynamics; RNA structure; SHAPE-seq; cotranscriptional RNA folding; molecular dynamics; signal recognition particle; toehold strand displacement; transcription.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Escherichia coli / chemistry*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • RNA Folding*
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / metabolism
  • Ribonuclease P / chemistry*
  • Ribonuclease P / metabolism
  • Signal Recognition Particle / chemistry*
  • Signal Recognition Particle / metabolism


  • Escherichia coli Proteins
  • RNA, Bacterial
  • Signal Recognition Particle
  • Ribonuclease P