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Nucleic Acids Symposium Series 2004 48(1):31-32; doi:10.1093/nass/48.1.31
© 2004 by Oxford University Press
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Development of a novel solvatochromic pyrimidine analog for probing local dielectric environment of DNA polymerase

Kazuki Tainaka1,3, Akimitsu Okamoto1,3 and Isao Saito2,3

1 Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 615-8510, Japan, 2 Faculty of Engineering, NEW CAT Institute, Nihon University, Koriyama 963-8642, Japan, 3 SORST, Japan Science and Technology Corporation

A novel uracil derivative tethering a solvatochromic chromophore, 6-dimethyl-2-acylnaphthalene (DAN), has been synthesized, and local dielectric constant in the recognition site of Klenow fragment (KF) has been investigated by steady-state fluorescence measurement using DNA substrates containing the solvatochromic uridine. Steady-state fluorescence measurements suggest that KF covers about 10 base pairs of the duplex DNA upstream of the primer terminus, and the vicinity of the incorporation site of triphosphate is the most hydrophobic environment.


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