Probing excited conformational states of nucleic acids by nitrogen CEST NMR spectroscopy

J Magn Reson. 2020 Jan:310:106642. doi: 10.1016/j.jmr.2019.106642. Epub 2019 Nov 11.

Abstract

Characterizing low-populated and short-lived excited conformational states has become increasingly important for understanding mechanisms of RNA function. Interconversion between RNA ground and excited conformational states often involves base pairing rearrangements that lead to changes in the hydrogen-bond network. Here, we present two 15N chemical exchange saturation transfer (CEST) NMR experiments that utilize protonated and non-protonated nitrogens, which are key hydrogen-bond donors and acceptors, for characterizing excited conformational states in RNA. We demonstrated these approaches on the B. Cereus fluoride riboswitch, where 15N CEST profiles complement 13C CEST profiles in depicting a potential pathway for ligand-dependent allosteric regulation of the excited conformational state of the fluoride riboswitch.

Keywords: Chemical exchange; Ligand binding; RNA dynamics; Riboswitch.

Publication types

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

MeSH terms

  • Algorithms
  • Bacillus cereus / chemistry
  • Fluorides / chemistry
  • Hydrogen Bonding
  • Ligands
  • Molecular Structure
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation*
  • Nucleic Acids / chemistry*
  • Protons
  • RNA, Bacterial / chemistry
  • Riboswitch

Substances

  • Ligands
  • Nitrogen Isotopes
  • Nucleic Acids
  • Protons
  • RNA, Bacterial
  • Riboswitch
  • Fluorides