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

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

4The nature of binding of Ru(phen) 3 2+ (I), Ru(bipy) 3 2+. (II), Ru(terpy) 2 2+ (III) (phen = 1,10-phenanthroline, bipy = 2,2′-bipyridyl, terpy = 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°±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 Mg 2+ 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.nonemixedJ. M. KELLY; TOSSI A.; D. J. MCCONNELL; C. OUUIGINJ. M., Kelly; Tossi, Alessandro; D. J., Mcconnell; C., Ouuigi

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

Ruthenium polypyridyl complexes: their interaction with DNA and their role as sensitisers for its photocleavage

The excited state of the 1,4,5,8-tetra-azaphenanthrene complex, [Ru(TAP)3]2+, which unlike [Ru(phen)3] 2+ (phen = 1,10-phenanthroline) or [Ru(bipy)3] 2+ (bipy = 2,2′-bipyridyl) is strongly quenched upon binding to poly[d(G-C)], is found to be much more effective than either [Ru(phen) 3]2+ or [Ru(bipy)3]2+ in causing cleavage of the DNA backbone.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Fluorescent Single-Stranded DNA Binding Protein as a Probe for Sensitive, Real-Time Assays of Helicase Activity

The formation and maintenance of single-stranded DNA (ssDNA) are essential parts of many processes involving DNA. For example, strand separation of double-stranded DNA (dsDNA) is catalyzed by helicases, and this exposure of the bases on the DNA allows further processing, such as replication, recombination, or repair. Assays of helicase activity and probes for their mechanism are essential for understanding related biological processes. Here we describe the development and use of a fluorescent probe to measure ssDNA formation specifically and in real time, with high sensitivity and time resolution. The reagentless biosensor is based on the ssDNA binding protein (SSB) from Escherichia coli, labeled at a specific site with a coumarin fluorophore. Its use in the study of DNA manipulations involving ssDNA intermediates is demonstrated in assays for DNA unwinding, catalyzed by DNA helicases