A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling

Biochem Biophys Res Commun. 2006 Apr 28;343(1):117-24. doi: 10.1016/j.bbrc.2006.02.138. Epub 2006 Mar 3.

Abstract

In RNA site-directed spin labeling (SDSL) studies, structural and dynamic information at the individual RNA nucleotide level is derived from the observed electron paramagnetic resonance spectrum of a covalently attached nitroxide. A systematic approach for RNA SDSL is to establish a library that categorizes observed spectral lineshapes based on known RNA structures, thus enabling lineshape-based structure identification at any RNA site. To establish the first RNA SDSL library, selective secondary structure elements have been systematically engineered into a model RNA. Nitroxide lineshapes reporting features specific to each element were obtained utilizing a new avidin-tethering scheme for suppressing spectral effects due to uniform RNA tumbling. The data demonstrated two key features required for a SDSL library with a predicting power: (i) spectral divergence--distinctive lineshape for different elements; and (ii) spectral convergence--similar lineshape for the same element in different contexts. This sets the foundation for further RNA SDSL library development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Avidin / chemistry
  • Base Pairing
  • Electron Spin Resonance Spectroscopy / methods*
  • Models, Molecular
  • Nitrogen Oxides / chemistry
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • Spin Labels*

Substances

  • Nitrogen Oxides
  • Spin Labels
  • Avidin
  • RNA
  • nitroxyl