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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 28, Number 12
BKCSDE 28(12)
December 20, 2007 

Meso-tetrakis(N-methylpyridinium-4-yl)porphyrin at the Minor Groove
of Contiguous Adenine-Thymine Base Pairs
Youn-Hee Chae, Biao Jin, Jong-Ki Kim, Sung Wook Han, Seog K. Kim, Hyun Mee Lee*
Meso-tetrakis(N-methylpyridinium-4-yl)porphyrin, DNA, Minor groove, Molecular dynamics
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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