5-Substituted Pyrimidine and 7-Substituted 7-Deazapurine dNTPs as Substrates for DNA Polymerases in Competitive Primer Extension in the Presence of Natural dNTPs.
A complete series of 5-substituted uracil or cytosine, as well as 7-substituted 7-deazaadenine and 7-deazaguanine 2'-deoxyribonucleoside triphosphates (dNTPs) bearing substituents of increasing bulkiness (H, Me, vinyl, ethynyl, and phenyl) were systematically studied in competitive primer extension in the presence of their natural counterparts (nonmodified dNTPs), and their kinetic data were determined. The results show that modified dNTPs bearing π-electron-containing substituents (vinyl, ethynyl, Ph) are typically excellent substrates for DNA polymerases comparable to or better than natural dNTPs. The kinetic studies revealed that these modified dNTPs have higher affinity to the active site of the enzyme-primer-template complex, and the calculations (semiempirical quantum mechanical scoring function) suggest that it is due to the cation-π interaction of the modified dNTP with Arg629 in the active site of Bst DNA polymerase.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
Hana
H
Cahová
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
Alessandro
A
Panattoni
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
Pavel
P
Kielkowski
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
Jindřich
J
Fanfrlík
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.|Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, Prague-2 12843, Czech Republic.
Michal
M
Hocek
D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D007700:Kinetics; D009711:Nucleotides / Q000737:chemistry*; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D011789:Quantum Theory; D013379:Substrate Specificity
C512929:7-deazapurine; D009711:Nucleotides; D011687:Purines; D011743:Pyrimidines; D004259:DNA-Directed DNA Polymerase