Direct identification of base-paired RNA nucleotides by correlated chemical probing

RNA. 2017 Jan;23(1):6-13. doi: 10.1261/rna.058586.116. Epub 2016 Nov 1.


Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base-pairing interactions. We recently introduced an approach for single-molecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP). RING-MaP experiments reveal diverse through-space interactions corresponding to both secondary and tertiary structure. Here we develop a framework for using RING-MaP data to directly and robustly identify canonical base pairs in RNA. When applied to three representative RNAs, this framework identified 20%-50% of accepted base pairs with a <10% false discovery rate, allowing detection of 88% of duplexes containing four or more base pairs, including pseudoknotted pairs. We further show that base pairs determined from RING-MaP analysis significantly improve secondary structure modeling. RING-MaP-based correlated chemical probing represents a direct, experimentally concise, and accurate approach for detection of individual base pairs and helices and should greatly facilitate structure modeling for complex RNAs.

Keywords: DMS reactivity; RNA secondary structure; chemical probing; pseudoknots; structure prediction.

Publication types

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

MeSH terms

  • Algorithms
  • Base Pairing
  • Models, Molecular
  • Mutation
  • Nucleic Acid Conformation
  • Nucleotides / genetics*
  • RNA / chemistry*
  • RNA / genetics
  • Software


  • Nucleotides
  • RNA