High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label

Nucleic Acids Res. 2020 Jan 24;48(2):924-933. doi: 10.1093/nar/gkz1096.

Abstract

Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing / genetics*
  • DNA / chemistry
  • DNA / isolation & purification*
  • Electron Spin Resonance Spectroscopy*
  • Isoindoles / chemistry
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA / isolation & purification*
  • Spin Labels

Substances

  • Isoindoles
  • Spin Labels
  • RNA
  • DNA