Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling

Biochemistry. 2014 Jun 10;53(22):3526-8. doi: 10.1021/bi500404b. Epub 2014 May 28.

Abstract

Site-directed spin labeling with continuous wave electron paramagnetic resonance (EPR) spectroscopy was utilized to characterize dynamic features of the kink-turn motif formed through a leader-linker interaction in the Vibrio cholerae glycine riboswitch. Efficient incorporation of spin-labels into select sites within the phosphate backbone of the leader-linker region proceeded via splinted ligation of chemically synthesized spin-labeled oligonucleotides to in vitro transcribed larger RNA fragments. The resultant nitroxide EPR line shapes have spectral characteristics consistent with a kink-turn motif and reveal differential backbone dynamics that are modulated by the presence of magnesium, potassium, and glycine.

Publication types

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

MeSH terms

  • 5' Untranslated Regions / physiology*
  • Electron Spin Resonance Spectroscopy
  • Glycine / genetics*
  • Glycine / metabolism*
  • Molecular Dynamics Simulation*
  • Protein Binding / physiology
  • RNA / genetics
  • Riboswitch / physiology*
  • Spin Labels*

Substances

  • 5' Untranslated Regions
  • Riboswitch
  • Spin Labels
  • RNA
  • Glycine