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Molecular simulation, v.29 no.2, 2003년, pp.83 - 89
Kang, Nam Sook (Department of Chemistry and CAMD Research Center, Soong Sil University, Seoul 156-743, South Korea) , No, Kyung Tai (Department of Chemistry and CAMD Research Center, Soong Sil University, Seoul 156-743, South Korea) , Jhon, Mu Shik (Department of Chemistry, Korea Advanced Institute of Science and Technology, 373-1 Kusung-dong Yusung-gu, Taejon 305-701, South Korea)
Molecular dynamics simulations were carried out for a right-handed and left-handed DNA heteropolymeric fragment, in which four different types of nucleotides constituted the sequence. The average structures obtained from the simulation converged to within ~1.4 Å rms fluctuation for the left-handed and for the right-handed DNA. The distribution of hydration sites and the hydrogen-bonded circular network of water molecules around guanine and cytosine bases were distinctively different in two DNA conformations. The hydrogen-bonded circular network, ring structure, of water molecules within 4.0 Å around two DNA molecules was better formed in the right-handed DNA than in the left-handed DNA, showing a higher ratio of hexameric ring to pentameric ring (R 6 /R 5 ).
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