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.