Development of a novel solvatochromic pyrimidine analog for probing local dielectric environment of DNA polymerase

Kazuki Tainaka; Akimitsu Okamoto; Isao Saito

doi:10.1093/nass/48.1.31

Development of a novel solvatochromic pyrimidine analog for probing local dielectric environment of DNA polymerase

Nucleic Acids Symp Ser (Oxf). 2004:(48):31-2. doi: 10.1093/nass/48.1.31.

Authors

Kazuki Tainaka¹, Akimitsu Okamoto, Isao Saito

Affiliation

¹ Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 615-8510, Japan.

PMID: 17150463
DOI: 10.1093/nass/48.1.31

Abstract

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.

MeSH terms

Binding Sites
Chemistry Techniques, Analytical / methods*
DNA Polymerase I / metabolism*
Electric Conductivity
Electrochemistry
Naphthalenes / chemistry
Spectrometry, Fluorescence
Uracil / analogs & derivatives*
Uracil / chemical synthesis*
Uracil / chemistry

Substances

Naphthalenes
naphthalene
Uracil
DNA Polymerase I