Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface

Methods Mol Biol. 2020:2113:251-262. doi: 10.1007/978-1-0716-0278-2_17.


Currently, studies of RNA/protein interactions occupy a prominent place in molecular biology and medicine. The structures of RNA-protein complexes may be determined by X-ray crystallography or NMR for further analyses. These methods are time-consuming and difficult due to the versatility and dynamics of the RNA structure. Furthermore, due to the need to solve the "phase problem" for each dataset in crystallography, crystallographic structures of RNA are still underrepresented. Structure determination of single ribonucleotide-protein complexes is a useful tool to identify the position of single-stranded RNA-binding sites in proteins. We describe here a structural approach that incorporates affinity measurement of a protein for various single ribonucleotides, ranking the RNA/protein complexes according to their stability. This chapter describes how to perform these measurements, including a perspective for the analysis of RNA-binding sites in protein and single-nucleotide crystal soaking.

Keywords: Crystal soaking; Fluorescence; Nucleotide–protein interactions; RNA-binding proteins; RNA–protein complexes; Ribonucleotide.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Membrane Proteins / chemistry*
  • Membrane Proteins / metabolism*
  • Models, Molecular
  • Protein Conformation
  • Protein Stability
  • RNA / metabolism*
  • Ribonucleotides / chemistry
  • Spectrometry, Fluorescence


  • Membrane Proteins
  • Ribonucleotides
  • RNA