Probing Sequence and Topological Specificity in the Binding of Tetra(Methylpyridyl)Porphines to DNAs

Abstract

The binding of a family of tetra(methylpyridyl)porphines to relaxed and supercoiled circular phiX197RF DNA has been probed using restriction endonuclease activity assays employing nine restriction enzymes (selected for different cleavage sequences and different flanking sequences), mung bean nuclease assays and E.coli topoisomerase assays. 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 flanking sequences affect the selectivity in binding. Mung bean digestion assays indicate that all three isomers alter the conformation of the supercoiled DNA, with the ortho isomer giving the greatest distortion. Topoisomerase studies suggest that these molecules unwind the DNA. 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.