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Nucleic Acids Symposium Series 2005 49(1):215-216; doi:10.1093/nass/49.1.215
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© 2005 Oxford University Press

Computational evaluation of the specific interaction between cation and mismatch base pair

Hajime Sugiyama1, Nobue Adachi2, Susumu Kawauchi3, Tetsuo Kozasa4, Takuma Katayama4, Hidetaka Torigoe4, Akira Ono5 and Yutaka Tamura6

1 Fujitsu Limited, 1-9-3 Nakase, Chiba 261-8588, Japan, 2 Fujitsu Laboratories Limited, 4-1-1 Kamikodanaka, Kawasaki 211-8588, Japan, 3 Tokyo Institute of Technology, 2-12-1 Oookayama, Tokyo 152-8552, Japan, 4 Tokyo University of Science, 1-3 Kagurazaka, Tokyo 162-8601, Japan, 5 Kanagawa University, 3-27-1 Rokkakubashi, Yokohama 221-8686, Japan, 6 National Institute of Advanced Industrial Science and Technology (AIST), 2-2-2 Marunouchi, Tokyo 100-0005, Japan

Ab initio calculations were carried out to characterize the structure and energetic of silver cation (Ag (I)) complex with cytosine (C:Ag:C) and mercury cation (Hg (II)) complex with thymine (T:Hg:T) systems. These metal-modified mismatch base pairs have been optimized using Hatree-Fock method without any symmetry constrains. Using above methods, the models of Ag (I) in a crosslink between O2 carbonyl oxygen of cytosine, O2(C):Ag:O2(C), and Hg (II) in a crosslink between N3 nitrogen atom of thymine, N3(T):Hg:N3(T) were obtained. Furthermore, the interaction energies of C:Ag:C and T:Hg:T models were estimated. The result showed that the coordination silver (I) cation with cytosine is more stable than hydrate state.


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