title: A small molecule affecting the replication of trinucleotide repeat d(GAA)n.
abstract: 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.
authors.affiliation: Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan.
authors.forename: Hanping
authors.initials: H
authors.lastname: He
authors.forename: Masaki
authors.initials: M
authors.lastname: Hagihara
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Nakatani
mesh_terms: D001483:Base Sequence; D004256:DNA Polymerase I / Q000378:metabolism; D004261:DNA Replication; D006801:Humans; D008958:Models, Molecular; D015394:Molecular Structure; D019914:Taq Polymerase / Q000378:metabolism; D018911:Trinucleotide Repeats / Q000187:drug effects*
chemical_list: D019914:Taq Polymerase; D004256:DNA Polymerase I