Nile Red nucleoside: design of a solvatofluorochromic nucleoside as an indicator of micropolarity around DNA.
The fluorophore, Nile Red, effectively works as a polarity-sensitive fluorescence probe. We have designed a new nucleoside modified by Nile Red for examining the change in the polarity of the microenvironment surrounding DNA. We synthesized a Nile Red nucleoside (1), formed by replacing nucleobases with Nile Red, through the coupling of a 2-hydroxylated Nile Red derivative and 1,2-dideoxyglycan. This nucleoside showed a high solvatofluorochromicity. The fluorescence of 1 incorporated into DNA was greatly shifted to shorter wavelength by the addition of beta-cyclodextrin. The photophysical function of the Nile Red nucleoside will be a good optical indicator for monitoring the change in the micropolarity properties at a specific site on target sequences with interaction between DNA and DNA-binding molecules.
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
Fujiwara
Yoshimasa
Y
D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D009705:Nucleosides / Q000138:chemical synthesis*; D010078:Oxazines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D047392:beta-Cyclodextrins / Q000737:chemistry
D005456:Fluorescent Dyes; D009705:Nucleosides; D010078:Oxazines; D047392:beta-Cyclodextrins; D004247:DNA; C031215:betadex; C044808:nile red