Open AccessNMR structural analysis of the G.G mismatch DNA complexed with naphthyridine-dimer
Author(s) -
Makoto Nomura,
Shinya Hagihara,
Yuki Goto,
Kazuhiko Nakatani,
Chojiro Kojima
Publication year - 2005
Publication title -
nucleic acids symposium series
Language(s) - English
Resource type - Journals
eISSN - 1746-8272
pISSN - 0261-3166
DOI - 10.1093/nass/49.1.213
Subject(s) - dimer , oligomer , hydrogen bond , crystallography , dna , stoichiometry , proton nmr , chemistry , helix (gastropod) , nmr spectra database , spectral line , stereochemistry , molecule , physics , polymer chemistry , biology , organic chemistry , biochemistry , snail , astronomy , ecology
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.
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