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

We report a novel fluorescent nucleobase, U-DNC, for the mapping of the local dielectric properties around DNA. Fluorescence spectra of the nucleoside d U-DNC 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 U-DNC.