Site-specific labeling of RNA with fluorophores and other structural probes

Methods. 1999 May;18(1):60-70. doi: 10.1006/meth.1999.0757.


Site-specific probes provide a powerful tool for structure and function studies of nucleic acids, especially in elucidating tertiary structures of large ribozymes and other folded RNA molecules. Among many types of extrinsic labels, fluorophores are most attractive because they can provide structural information at millisecond time resolution, thus allowing real-time observation of structural transition during biological function. Methods for introducing fluorophores in RNA molecules are summarized here. These methods are robust and readily applicable to the labeling of other types of probes. However, as each case of RNA modification is unique, fine tuning of the general methodology is beneficial.

Publication types

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

MeSH terms

  • Amines / chemistry
  • Fluoresceins / chemistry
  • Fluorescent Dyes / metabolism*
  • Models, Chemical
  • Models, Genetic
  • Molecular Biology / methods*
  • Oligonucleotides / metabolism
  • RNA / metabolism*
  • Sulfhydryl Compounds / chemistry


  • Amines
  • Fluoresceins
  • Fluorescent Dyes
  • Oligonucleotides
  • Sulfhydryl Compounds
  • RNA