Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Meso-tetrakis(N-methylpyridinium-4-yl)porphyrin at the Minor Groove of Contiguous Adenine-Thymine Base Pairs

  • Chae, Youn-Hee (Department of Chemistry, College of Sciences, Yeungnam University) ;
  • Jin, Biao (Department of Chemistry, College of Sciences, Yeungnam University) ;
  • Kim, Jong-Ki (Department of Biomedical Engineering, School of Medicine, Catholic University of Daegu) ;
  • Han, Sung-Wook (School of Herb Medicine Resource, Kyungwoon University) ;
  • Kim, Seog-K. (Department of Chemistry, College of Sciences, Yeungnam University) ;
  • Lee, Hyun-Mee (Department of Chemistry, College of Sciences, Yeungnam University)
  • Published : 2007.12.20
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Abstract

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.

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References

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