Fluorescence reporters for Hfq oligomerization and RNA annealing

Subrata Panja, Sarah A. Woodson

Research output: Contribution to journalArticlepeer-review


Fluorescence spectroscopy is a sensitive technique for detecting protein-protein, protein-RNA, and RNA-RNA interactions, requiring only nanomolar concentrations of labeled components. Fluorescence anisotropy provides information about the assembly of multi-subunit proteins, while molecular beacons provide a sensitive and quantitative reporter for base pairing between complementary RNAs. Here we present a detailed protocol for labeling Hfq protein with cyanine 3-maleimide and dansyl chloride to study the protein oligomerization and RNA binding by semi-native polyacrylamide gel electrophoresis (PAGE) and fl uorescence anisotropy. We also present a detailed protocol for measuring the rate of annealing between a molecular beacon and a target RNA in the presence of Hfq using a stopped-fl ow spectrometer.

Original languageEnglish (US)
Pages (from-to)369-383
Number of pages15
JournalMethods in molecular biology (Clifton, N.J.)
StatePublished - 2015


  • Fluorescence anisotropy
  • Hfq
  • Molecular beacon
  • Protein oligomerization
  • RNA chaperone
  • Stopped-fl ow fl uorescence

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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