A high-throughput fluorescence screen to monitor the specific binding of antagonists to RNA targets

Keita Hamasaki, Robert R. Rando

Research output: Contribution to journalArticle

39 Citations (Scopus)


Since RNA molecules can form intricate three-dimensional structures, it should be possible to design specific, high-affinity antagonists directed against these structures. To begin to explore the validity of this possibility, high-throughput screening methods are required to assay for RNA antagonists. A fluorescence quenching technique is described here in a 96- well plate format which is capable of screening chemical diversity libraries. A pyrene-containing aminoglycoside analog is used to accurately monitor antagonist binding to a prokaryotic 16S rRNA A-site decoding region construct. This rRNA region comprises the natural target for aminoglycoside antibiotics. The fluorescence technique reported here should be generally adaptable to monitor the binding of structurally novel antagonists to any selected RNA target.

Original languageEnglish
Pages (from-to)183-190
Number of pages8
JournalAnalytical Biochemistry
Issue number2
Publication statusPublished - 1998 Aug 1


ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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