Abstract
Investigations were carried out to look into the system of host + guest as a ligand targeted to the duplex DNA. The possible structures of host RhB-β-CDen were studied by minimization and molecular dynamics simulation. In the association state of host + guest (1:1) system, the guest molecule of 1-borneol could insert into the cyclodextrin cavity of the host molecule RhB-β-CDen. The interactive sites of the RhB-β-CDen + borneol system as a ligand targeting to the duplex DNA d(C)8·d(G)8 were obtained by docking interaction. It was found that the ligand was probably bound to the duplex DNA in the minor groove. The conformations of DNA varies noticeably to accommodate the binding groups of the ligand. Water molecules bridge between the bases of duplex DNA and/or ligand by hydrogen bonds to make the entire system more stable.
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