Structure Determination of an Ag<sup>I</sup>‐Mediated Cytosine–Cytosine Base Pair within DNA Duplex in Solution with <sup>1</sup>H/<sup>15</sup>N/<sup>109</sup>Ag NMR Spectroscopy

  • Takenori Dairaku
    School of Pharmaceutical Sciences Ohu University 31-1 Misumido, Tomita-machi, Koriyama Fukushima 963-8611 Japan
  • Kyoko Furuita
    Institute for Protein Research Osaka University 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
  • Hajime Sato
    Application, Bruker BioSpin K. K. 3–9 Moriya-cho, Kanagawa-ku, Yokohama Kanagawa 221-0022 Japan
  • Jakub Šebera
    Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, v.v.i. Flemingovo náměstí 2 16610 Praha 6 Czech Republic
  • Katsuyuki Nakashima
    Faculty of Phamaceutical Scienes Tokushima Bunri University Yamashiro-cho Tokushima 770-8514 Japan
  • Jiro Kondo
    Department of Materials and Life Sciences Faculty of Science and Technology, Sophia University 7-1 Kioi-cho, Chiyoda-ku Tokyo 102-8554 Japan
  • Daichi Yamanaka
    Graduate School of Pharmaceutical Sciences Tohoku University 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
  • Yoshinori Kondo
    Graduate School of Pharmaceutical Sciences Tohoku University 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
  • Itaru Okamoto
    Department of Material & Life Chemistry, Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
  • Akira Ono
    Department of Material & Life Chemistry, Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
  • Vladimír Sychrovský
    Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, v.v.i. Flemingovo náměstí 2 16610 Praha 6 Czech Republic
  • Chojiro Kojima
    Institute for Protein Research Osaka University 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
  • Yoshiyuki Tanaka
    Graduate School of Pharmaceutical Sciences Tohoku University 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan

Abstract

<jats:title>Abstract</jats:title><jats:p>The structure of an Ag<jats:sup>I</jats:sup>‐mediated cytosine–cytosine base pair, C–Ag<jats:sup>I</jats:sup>–C, was determined with NMR spectroscopy in solution. The observation of 1‐bond <jats:sup>15</jats:sup>N‐<jats:sup>109</jats:sup>Ag <jats:italic>J</jats:italic>‐coupling (<jats:sup>1</jats:sup><jats:italic>J</jats:italic>(<jats:sup>15</jats:sup>N,<jats:sup>109</jats:sup>Ag): 83 and 84 Hz) recorded within the C–Ag<jats:sup>I</jats:sup>–C base pair evidenced the N3–Ag<jats:sup>I</jats:sup>–N3 linkage in C–Ag<jats:sup>I</jats:sup>–C. The triplet resonances of the N4 atoms in C–Ag<jats:sup>I</jats:sup>–C demonstrated that each exocyclic N4 atom exists as an amino group (−NH<jats:sub>2</jats:sub>), and any isomerization and/or N4–Ag<jats:sup>I</jats:sup> bonding can be excluded. The 3D structure of Ag<jats:sup>I</jats:sup>–DNA complex determined with NOEs was classified as a B‐form conformation with a notable propeller twist of C–Ag<jats:sup>I</jats:sup>–C (−18.3±3.0°). The <jats:sup>109</jats:sup>Ag NMR chemical shift of C‐Ag<jats:sup>I</jats:sup>‐C was recorded for cytidine/Ag<jats:sup>I</jats:sup> complex (<jats:italic>δ</jats:italic>(<jats:sup>109</jats:sup>Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C–Ag<jats:sup>I</jats:sup>–C base pair.</jats:p>

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