Role of a non-natural -C-nucleotide unit in DNA as a te...

Role of a non-natural -C-nucleotide unit in DNA as a template for DNA and RNA syntheses and as a substrate for nucleolytic digestion

Role of a non-natural -C-nucleotide unit in DNA as a template for DNA and RNA syntheses and as a substrate for nucleolytic digestion
September 2003
Saeko Aketania, Kentaro Tanakaa, Kaneyoshi Yamamotob, Akira Ishihamab, Honghua Caoc, Atsushi Tengeijia and Mitsuhiko Shionoya
European Journal of Pharmaceutical Sciences
Abstract
A non-natural -C-nucleoside bearing a 3,4-dibenzyloxyphenyl group as a nucleobase (X) was synthesized and incorporated into a 34-mer oligomer with the sequence 5'-dTTTTTAAAAAAXATATAGCAGCGACATGTCACCG-3'. This synthetic oligonucleotide was examined for template activity in the enzymatic syntheses of DNA by the Klenow fragments of Escherichia coli DNA polymerase I and the recombinant DNA polymerase I, and in the synthesis of RNA by the E. coli RNA polymerase core enzyme. As a result, the template-directed polymerization of both DNA and RNA was precisely terminated at the position of X. The X-containing oligonucleotide was also tested for digestion by an exonuclease, Exo III nuclease (Exo III), and an endonuclease, Mung Bean nuclease (MB). The results indicate that the artificial nucleobase X acts as a terminator for digestion by Exo III, whereas the site X becomes susceptible to digestion by MB. These findings provide a useful tool for the size control of products in the synthesis and degradation of nucleic acids.
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