RNA Folding

Volume 1086 of the series Methods in Molecular Biology pp 53-77


The Mutate-and-Map Protocol for Inferring Base Pairs in Structured RNA

  • Pablo CorderoAffiliated withDepartment of Biomedical Informatics, Stanford University
  • , Wipapat KladwangAffiliated withDepartment of Biochemistry, Stanford University
  • , Christopher C. VanLangAffiliated withDepartment of Chemical Engineering, Stanford University
  • , Rhiju DasAffiliated withDepartment of Biochemistry, Stanford UniversityDepartment of Physics, Stanford University

* Final gross prices may vary according to local VAT.

Get Access


Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule’s reactivity to different probes is quantified at single nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strategies for high-throughput readouts, chemical modification, and rapid data analysis. Recently, we have coupled the technique to high-throughput mutagenesis. Point mutations of a base paired nucleotide can lead to exposure of not only that nucleotide but also its interaction partner. Systematically carrying out the mutation and mapping for the entire system gives an experimental approximation of the molecule’s “contact map.” Here, we give our in-house protocol for this “mutate-and-map” (M2) strategy, based on 96-well capillary electrophoresis, and we provide practical tips on interpreting the data to infer nucleic acid structure.

Key words

RNA structure Chemical mapping Capillary sequencing Systematic mutation