PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure

J Am Chem Soc. 2010 Feb 10;132(5):1454-5. doi: 10.1021/ja9077914.

Abstract

Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spin labels at positions U4-U14, U4-U15, U14-U26, and U15-U26 were unchanged upon neomycin binding which implies that the global stem-loop architecture is preserved in the absence and presence of the ligand. On the basis of our results, we infer that low-temperature PELDOR data unambiguously demonstrate the existence of an enthalpically favorable set of RNA conformations ready to bind the ligand without major global rearrangement.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / metabolism*
  • Electron Spin Resonance Spectroscopy / methods*
  • Neomycin / metabolism*
  • Nucleic Acid Conformation
  • Protein Binding
  • RNA / analysis*
  • RNA / metabolism
  • Spin Labels
  • Uridine / analysis

Substances

  • Anti-Bacterial Agents
  • Spin Labels
  • RNA
  • Neomycin
  • Uridine