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Nucleic Acids Symposium Series 2005 49(1):49-50; doi:10.1093/nass/49.1.49
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© 2005 Oxford University Press

Solution structure of a small-molecular ligand complexed with CAG trinucleotide repeat DNA

Kazuhiko Nakatani1,2, Shinya Hagihara1, Yuki Goto1, Akio Kobori1, Masaki Hagihara1, Gosuke Hayashi1, Motoki Kyo3, Makoto Nomura4, Masaki Mishima4 and Chojiro Kojima4

1 Graduate School of Engineering, Kyoto University, Kyoto 618-8510, Japan, 2 PRESTO (JST), Tsuruga, Fukui 914-0047, Japan, 3 Toyobo Co. Ltd., Tsuruga, Fukui 914-0047, Japan, 4 Graduate School of Biological Science, Nara Institute of Science and Technology, Nara 630-0192, Japan

NMR structure of the first identified ligand, naphthyridine–azaquinolone (NA), complexed with the CAG-CAG triad is reported. The determined structure revealed the invasive ligands binding to the A-A mismatch and flanking G-C base pairs, causing the widowed cytosines to flip out from {pi}-stack. Hydrogen-bond pairs between NA and DNA, naphthyridine-guanine and azaquinolone-adenine, are well stacked in the right-handed DNA helix, showing structural mimicry of Watson–Crick base pairing. This is the first observation that the small molecular ligand induced the base flipping of the nucleotide base in the Watson-Crick base pair.


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