Sequence-selective binding of an ellipticine derivative to DNA.

The DNA sequence specificity of an ellipticine derivative bearing an aminoalkyl side chain has been determined by a variety of footprinting methods. The drug exhibits sequence selective binding and discriminates against runs of adenines or thymines. Binding is shown to occur at various sequences with a preference for GC rich regions of DNA. A large enhancement of DNAase I and of hydroxyl radical cleavage in regions rich in A's or T's is observed together with hyperreactivity of adenines towards diethylpyrocarbonate in the presence of drug. This indicates the occurrence of drug-induced changes in critical conformational features of DNA. The total absence of hyperreactivity of guanine residues towards diethylpyrocarbonate appears to be related to the sequence selectivity of drug binding. No alteration of the dimethyl sulphate and methylene blue-induced cleavage of DNA is observed. Irradiation of ellipticine derivative-DNA complexes with UV light followed by alkali treatment leads to selective photocleavage at guanine residues, consistent with the deduced degree of selectivity of the binding reaction.

Methylene blue photosensitised strand cleavage of DNA: effects of dye binding and oxygen.

It is shown that methylene blue (MB+) photosensitises DNA in either aerated or deaerated solutions, causing direct cleavage of phosphodiester bonds and rendering additional bonds labile to alkali. Evidence from unwinding and fluorimetric studies indicates that MB+ binds to DNA in at least 2 ways. Intercalation, which optimally induces helical unwinding of 24 degrees +/- 2 degrees per MB+, is markedly reduced upon neutralisation by Mg2+ of the DNA phosphates, while significant non-intercalative binding persists as shown by substantial fluorescence quenching at Mg2+ concentrations where there is little unwinding. MB+ induces photolysis at both low and high Mg2+ concentration - intercalation is apparently not required for photolysis. The quantum yield for strand breakage varies from 1-3 X 10(-7) under different conditions and is oxygen enhanced. The DNA cleavage is guanine specific. The 3' termini of the primary MB+-induced DNA photoproducts, unlike those generated by chemical sequencing retain an alkali labile adduct on the terminal phosphate.

A study of the interactions of some polypyridylruthenium (II) complexes with DNA using fluorescence spectroscopy, topoisomerisation and thermal denaturation.

The nature of binding of Ru(phen) 2+ (I), Ru(bipy) 2+ (II), Ru(terpy) 2+ (III) (phen = 1,10-phenanthroline, bipy 3 = 2,2'-bipyridyl, 3 terpy = 2,2'2," - 2 terpyridyl) to DNA, poly[d(G-C)] and poly[d(A-T)] has been compared by absorption, fluorescence, DNA melting and DNA unwinding techniques. I binds intercalatively to DNA in low ionic strength solutions. Topoisomerisation shows that it unwinds DNA by 22 degrees +/- 1 per residue and that it thermally stabilizes poly[d(A-T)] in a manner closely resembling ethidium. Poly[d(A-T)] induces greater spectral changes on I than poly[d(G-C)] and a preference for A-T rich regions is indicated. I binding is very sensitive to Mg2+ concentration. In contrast to I the binding of II and III appears to be mainly electrostatic in nature, and causes no unwinding. There is no evidence for the binding of the neutral Ru(phen)2 (CN)2 or Ru(bipy)2 (CN)2 complexes. DNA is cleaved, upon visible irradiation of aerated solutions, in the presence of either I or II.

A comparative study of the interaction of 5,10,15,20-tetrakis (N-methylpyridinium-4-yl)porphyrin and its zinc complex with DNA using fluorescence spectroscopy and topoisomerisation.

Binding of 5,10,15,20-tetrakis (N-methylpyridinium-4-yl)porphyrin (H2TMPyP4+) and its zinc complex (ZnTMPyP4+) to DNA is demonstrated by their coelectrophoresis and by absorption and fluorescence spectroscopic methods. Topoisomerisation of pBR322 DNA shows that H2TMPyP4+ unwinds DNA as efficiently as ethidium bromide showing that it intercalates at many sites. ZnTMPyP4+ may cause limited unwinding. Marked changes in the fluorescence spectra of the porphyrins are found in the presence of DNA. The fluorescence intensity of either H2TMPyP4+ or ZnTMPyP4+ is enhanced in the presence of poly (d(A-T)), whereas in the presence of poly (d(G-C] the fluorescence intensity of ZnTMPyP4+ is only slightly affected and that of H2TMPyP4+ markedly reduced. Both the porphyrins photosensitize the cleavage of DNA in aerated solution upon visible light irradiation.