• YAKHAK HOEJI
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• v.39 no.1
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• pp.78-84
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• 1995

Based on Computer graphics molecular modeling method, quinolone derivatives as DNA-gyrase inhibitors formed stable DNA-intercalation complex with deoxycytidilyl-3',5'-deoxy guanosine[d($C_{p}G)_{2}$] dinucleotide. When d($C_{p}G)_{2}$ and d($A_{p}T)_{2}$, were compared in order to find out which DNA could form more stable DNA-Drug complex based on interaction energy($\Delta$E) and DNA-Drug complex energy, d($C_{p}G)_{2}$ resulted in lower energy than d($A_{p}T)_{2}$.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2203-2208
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• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.