NMR structural analysis of the G.G mismatch DNA complexed with naphthyridine-dimer.
Naphthyridine-dimer (ND) specifically recognizes G.G mismatch DNA (Figure 1). However, its detailed recognition mechanism is not clear. Here a DNA oligomer d(CTAACGGAATG)/d(CATTCGGTTAA) complexed with ND was studied by NMR. The stoichiometry of DNA to ND was determined to be 1:2 at NMR concentration (2.5 mM). Proton resonances were completely assigned including H5' and H5'' using 1H-1H and 1H-13C 2D spectra of the complex. These spectra showed that four naphthyridine rings are staked in the helix and form hydrogen bonds with the four G residues in CGG/CGG region. These results indicate ND can specifically recognize the CGG/CGG sequence.
Nomura
Makoto
M
Graduate School of Biological Science, Nara Institute of Science and Technology, Nara 630-0101, Japan.
Hagihara
Shinya
S
Goto
Yuki
Y
Nakatani
Kazuhiko
K
Kojima
Chojiro
C
D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry; D006147:Guanine / Q000737:chemistry*; D009287:Naphthyridines / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular
D009287:Naphthyridines; C520211:bis((7-methylnaphthyridin-2-yl)carbamoylethyl)amine; D006147:Guanine; D004247:DNA