A dielectric-sensitive fluorescent DNA probe for monitoring polarities on the interior of a DNA-binding protein

Bioconjug Chem. 2005 Sep-Oct;16(5):1105-11. doi: 10.1021/bc050077i.

Abstract

We report a novel fluorescent nucleobase, (DNC)U, for the mapping of the local dielectric properties around DNA. Fluorescence spectra of the nucleoside d(DNC)U showed a significant shift depending on the solvent polarity. This property was used to determine the dielectric constants of the interior of DNA-binding proteins, such as DNA polymerases. We were able to demonstrate that the DNA-binding region of the Klenow fragment is a lower polarity site, as shown by the blue shift of the fluorescence peak originating from (DNC)U.

MeSH terms

  • Base Sequence
  • DNA Polymerase I / chemistry
  • DNA Polymerase I / metabolism
  • DNA Probes / chemistry*
  • DNA Probes / genetics
  • DNA Probes / metabolism*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism*
  • Fluorescent Dyes / chemistry*
  • Hydrogen Bonding
  • Molecular Structure
  • Spectrum Analysis

Substances

  • DNA Probes
  • DNA-Binding Proteins
  • Fluorescent Dyes
  • DNA Polymerase I