Dispersion of meso-tetrakis( N-methylpyridinium-4-yl)porphyrin on [d(A-T) n] 2 oligonucleotides

Abstract

The binding modes of the free-base meso-tetrakis( N-methylpyridinium-4-yl)porphyrin (TMPyP) complexed with [d(AT) n ] 2 oligonucleotides (where n = 3–8, corresponding to 6 to 16 AT base pairs) were studied by circular dichroism (CD). When associated with the shortest oligonucleotide, ([d(AT) 3] 2), a bisignate CD spectrum was produced in the Soret absorption region at the mixing ratio between 2.0 and 0.25, corresponding to one TMPyP per 0.5 to 4 oligonucleotides. Apparent bisignate CD was attributed to a stacked TMPyP along the DNA. On the other hand, when the oligonucleotide length reaches one helical turn or longer, ([d(AT) n ] 2, n = 6,7,8), TMPyP exhibited a positive CD signal, that corresponds to the monomeric groove binding mode, at the mixing ratio below 1.0 (one TMPyP per oligonucleotide). As the mixing ratio increases, the CD signal was best accounted for by the sum of the stacked and groove-binding TMPyP. At the intermediate oligonucleotide length ([d(AT) n ] 2, n = 4,5), the CD spectrum appeared to be the sum of the stacked and groove binding TMPyP at all mixing ratios. Therefore, it is conclusive that the full dispersion of TMPyP requires at least one helical turn of the AT sequence at a mixing ratio below 1.0. Further increase of the mixing ratio resulted in the stacking of TMPyP even at the long oligonucleotides.