期刊
CHEMISTRY-A EUROPEAN JOURNAL
卷 15, 期 40, 页码 10641-10648出版社
WILEY-BLACKWELL
DOI: 10.1002/chem.200901088
关键词
DNA recognition; ligand design; nucleotides; polymerases; small molecules
资金
- Japan Society for the Promotion of Science (JSPS) [18105006, 06061]
A newly designed ligand, methylcarbamoylnaphthyridine dimer (MCND), was synthesized and characterized. Ligand binding to d(GAA)(10) was investigated by UV thermal denaturation, circular dichroism spectroscopy, surface plasmon resonance, and cold-spray-ionization time-of-flight mass spectrometry. The results indicated that MCND bound to the d(GAA)(n) repeat to form a stable hairpin structure with a major binding stoichiometry of 3:1. The most likely binding site was identified as the G-G mismatch in the AGA/AGA triad. The polymerase stop assay showed that MCND binding to the d(GAA)(n) repeat effectively interfered with the extension of the primer at the first two GAA sites on the template with both prokaryotic Taq DNA polymerase and human DNA polymerase alpha.
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