Ab. Guliaev et Nb. Leontis, Cationic 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin fully intercalates at 5 '-CG-3 ' steps of duplex DNA in solution, BIOCHEM, 38(47), 1999, pp. 15425-15437
The interaction of 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)p (T4MPyP(4)) with the oligonucleotide DNA duplex [d(GCACGTGC)](2) was studied by two-
dimensional H-1 NMR spectroscopy, optical absorbance, circular dichroism, a
nd molecular dynamics simulation employing particle mesh Ewald methods. T4M
PyP(4+) is one of the largest aromatic molecules for which intercalative bi
nding to DNA has been proposed, although this has been called into question
by recent X-ray crystallographic work [Lipscomb et al. (1996) Biochemistry
35, 2818-2823]. T4MPyP(4+) binding to [d(GCACGTGC)](2) produced a single s
et of (mostly) upfield-shifted DNA resonances in slow exchange with the res
onances of the free DNA. Intra- and intermolecular NOEs observed in the com
plex showed that the porphyrin intercalates at the central 5'-CG-3' step of
the DNA duplex without disrupting the flanking base pairs. Absorption and
circular dichroism spectra of the complex also support intercalative bindin
g. Molecular dynamics simulations (using explicit solvent and PME methods),
carried out for fully and partially intercalated complexes, yielded stable
trajectories and plausible structures, but only the symmetrical, fully int
ercalated model agreed with NOESY data. Stable hydrogen bonding was observe
d during 600 ps of MD simulation for the base pairs flanking the binding si
te.