Pyridyl porphyrins have gained attention as potential antitumor agents. In this study we report on the binding of family of tetra(methylpyridyl)porphines to relaxed and supercoiled circular phiX197RF DNA. Binding to this DNAs was probed using restriction endonuclease activity assays employing nine restriction enzymes selected for different cleavage sequences and different flanking sequences. Use of a mixture of supercoiled and relaxed DNAs allowed for observation of topological and sequence effects in the binding. The restriction enzyme assays indicate that placement of the methyl substituent alters the sequence and topological specificity of binding. For example, the the restriction enzyme Mlu I (cleavage site ACGCGT), the ortho isomer yields partial inhibition of cleavage of supercoiled and relaxed DNA, the meta isomer yields inhibition of the relaxed DNA and no effect with supercoiled DNA, and the para isomer gives enhanced cleavage of supercoiled and relaxed DNA. With Dra I (TTTAAA), the ortho isomer again gives partial inhibition cleavage of supercoiled and relaxed DNA, the meta isomer gives inhibition of cleavage of relaxed AND supercoiled DNA, and the para isomer has no effect on cleavage of either form. Variations in the sequences flanking the restriction enzyme cleavage sites affect the selectivity in binding.  Molecular modeling suggests that the placement of the methyl substituent on the pyridyl rings affects the planarity of the molecules, which may alter the binding to DNA and lead to the observations above. Modeling studies also suggest differences in the mode of binding, e.g., the meta may bind by partial intercalation while the ortho prefers groove binding. This observation is supported by topoisomerase assays in which the meta and para isomers unwind the DNA while the ortho doe not. Binding constants for binding to salmon sperm DNA, obtained from uv titrations, are similar [circa 3 x 10<sup>4</sup> at 25 C]. Optical titration vs. temperature studies and isothermal calorimetry results suggest that the isomers bind with different enthalpies. The combined results of these studies demonstrate that the binding modes and specificities of these porphyrins  are structurally dependent.

Sequence and topological specificity in the binding of tetra(N-methylpyridyl)porphines to DNAs

249th National Meeting (2015)

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