title: Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA.
abstract: Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag(+) ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag(+) ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag(+) ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 10(6) M(-1) binding constant, which was significantly larger than those for nonspecific metal ion-DNA interactions. The specific binding between the Ag(+) ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag(+) ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag(+) binding. The binding affinity for the second Ag(+) binding was similar to that for the first Ag(+) binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag(+) ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.
authors.affiliation: Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan. htorigoe@rs.kagu.tus.ac.jp
authors.forename: Hidetaka
authors.initials: H
authors.lastname: Torigoe
authors.forename: Yukako
authors.initials: Y
authors.lastname: Miyakawa
authors.forename: Akira
authors.initials: A
authors.lastname: Ono
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Kozasa
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D008969:Molecular Sequence Data; D036103:Nanotechnology; D012834:Silver / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D007477:Ions; D012834:Silver; D004247:DNA