Standardization of RNA chemical mapping experiments

Biochemistry. 2014 May 20;53(19):3063-5. doi: 10.1021/bi5003426. Epub 2014 May 7.


Chemical mapping experiments offer powerful information about RNA structure but currently involve ad hoc assumptions in data processing. We show that simple dilutions, referencing standards (GAGUA hairpins), and HiTRACE/MAPseeker analysis allow rigorous overmodification correction, background subtraction, and normalization for electrophoretic data and a ligation bias correction needed for accurate deep sequencing data. Comparisons across six noncoding RNAs stringently test the proposed standardization of dimethyl sulfate (DMS), 2'-OH acylation (SHAPE), and carbodiimide measurements. Identification of new signatures for extrahelical bulges and DMS "hot spot" pockets (including tRNA A58, methylated in vivo) illustrates the utility and necessity of standardization for quantitative RNA mapping.

Publication types

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

MeSH terms

  • Acylation
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • Sulfuric Acid Esters / chemistry*


  • Sulfuric Acid Esters
  • RNA
  • dimethyl sulfate