A dielectric-sensitive fluorescent DNA probe for monitoring polarities on the interior of a DNA-binding protein.
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.
Okamoto
Akimitsu
A
Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 615-8510, Japan. okamoto@sbchem.kyoto-u.ac.jp
Tainaka
Kazuki
K
Saito
Isao
I
D001483:Base Sequence; D004256:DNA Polymerase I / Q000737:chemistry / Q000378:metabolism; D015342:DNA Probes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000737:chemistry*; D006860:Hydrogen Bonding; D015394:Molecular Structure; D013057:Spectrum Analysis
D015342:DNA Probes; D004268:DNA-Binding Proteins; D005456:Fluorescent Dyes; D004256:DNA Polymerase I