Dynamics and ordering in a spin-labeled oligonucleotide observed by 220 GHz electron paramagnetic resonance

Biophys J. 2000 Jan;78(1):430-8. doi: 10.1016/S0006-3495(00)76605-7.

Abstract

The dynamics of a newly synthesized cytosine spin-label and the spin-labeled pentamer TTC*TT have been observed by high-frequency (220 GHz) electron paramagnetic resonance (EPR) in aqueous solution at ambient temperature using only nanomolar amounts of spin-label. Temperature studies were carried out for both labeled species in buffer containing glycerol. The motion of the spin-labeled monomer could be fitted using a model of fully anisotropic rotation (FAR) over the entire temperature range studied. In the single-stranded pentamer, the high-field spectra are best interpreted using a model of microscopic ordering with macroscopic disorder (MOMD) with the probe in a highly nonpolar environment. The observed local order parameters of 0.60-0.70 suggest a micelle-like structure in which the label is tightly packed with the hydrophobic bases. These preliminary studies illustrate how the excellent orientation selectivity of high-field EPR provides new dynamic information about local base motions in DNA, and also how high-field EPR of spin-labels allows one to discriminate accurately between the effects of local versus global motions in spin-labeled macromolecules.

Publication types

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

MeSH terms

  • Base Sequence
  • Electron Spin Resonance Spectroscopy / methods
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / chemistry*
  • Spin Labels
  • Thermodynamics

Substances

  • Oligodeoxyribonucleotides
  • Spin Labels