Drug—DNA sequence‐dependent interactions analysed by electric linear dichroism

Abstract

The interactions between 20 drugs and a variety of synthetic DNA polymers and natural DNAs were studied by electric linear dichroism (ELD). All compounds tested, including several clinically used antitumour agents, are thought to exert their biological activities mainly by virtue of their abilities to bind to DNA. The selected drugs include intercalating agents with fused and unfused aromatic structures and several groove binders. To examine the role of base composition and base sequence in the binding of these drugs to DNA, ELD experiments were carried out with natural DNAs of widely differing base composition as well as with polynucleotides containing defined alternating and non-alternating repeating sequences, poly(dA).poly(dT), poly(dA-dT).poly(dA-dT),poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC). Among intercalating agents, actinomycin D was found to be by far the most GC-selective. GC selectivity was also observed with an amsacrine-4-carboxamide derivative and to a lesser extent with methylene blue. In contrast, the binding of amsacrine and 9-aminoacridine was practically unaffected by varying the GC content of the DNAs. Ethidium bromide, proflavine, mitoxantrone, daunomycin and an ellipticine derivative were found to bind best to alternating purine-pyrimidine sequences regardless of their nature. ELD measurements provided evidence for non-specific intercalation of amiloride. A significant AT selectivity was observed with hycanthone and lucanthone. The triphenyl methane dye methyl green was found to exhibit positive and negative dichroism signals at AT and GC sites, respectively, showing that the mode of binding of a drug can change markedly with the DNA base composition. Among minor groove binders, the N-methylpyrrole carboxamide-containing antibiotics netropsin and distamycin bound to DNA with very pronounced AT specificity, as expected. More interestingly the dye Hoechst 33258, berenil and a thiazole-containing lexitropsin elicited negative reduced dichroism in the presence of GC-rich DNA which is totally inconsistent with a groove binding process. We postulate that these three drugs share with the trypanocide 4',6-diamidino-2-phenylindole (DAPI) the property of intercalating at GC-rich sites and binding to the minor groove of DNA at other sites. Replacement of guanines by inosines (i.e., removal of the protruding exocyclic C-2 amino group of guanine) restored minor groove binding of DAPI, Hoechst 33258 and berenil. Thus there are several cases where the mode of binding to DNA is directly dependent on the base composition of the polymer. Consequently the ELD technique appears uniquely valuable as a means of investigating the possibility of sequence-dependent recognition of DNA by drugs.

Apparent circular dichroism signature of stirring-oriented DNA and drug–DNA complexes

“…Therefore, a negative LD contribution allied to the respective absorption bands of the intercalated ligand molecules can be expected. In full concordance with this, typical DNA intercalators such as proflavine [13], ethidium bromide [13], and ellipticine [14] display negative LD bands in stirring-oriented DNA sample (Fig. 2) indicating that the - * transition moments of the bound species are oriented perpendicular to the helix axis.…”

Analysing DNA complexes by circular and linear dichroism

“…A strong argument that the exocyclic amino group of guanine (Fig. 6) is responsible for the prevention of minor-groove binding of DAPI, APF (and other minor groove binders including Hoechst 33258) to [poly(dG-dC)I2 is the observation by Bailly et al (1992) and Sehlstedt et al (1993a) that minor groove binding geometry is restored in [poly(dI-dC)], (with inosine being a guanine devoid of the amino group). Thus, in the IC sequence DAPI is characterised by a positive LD with an amplitude that corresponds to an angle of 45-50" between its long axis and the DNA helix axis, a strong increase in fluorescence intensity and a shielding to quencher that indicates deep inclusion in the minor groove (Sehlstedt et a/., 1993b).…”

“…The similarity between the [poly(dG-dC)I2 and DNA results suggest that the drug has a tendency to prefer G C sequences. This type of inference, drawn from a comparison of LD results for complexes of a drug with DNAs of varying base composition, provides a possible tool for screening of sequence-dependent recognition (Bailly et al, 1992). Switching of binding mode, upon increasing the size of a potential intercalating plane, has also been found with trigonal, substitution inert metal complexes, such as [RuX2YI2+ (Friedman et al 1991).…”

PKD1 Unusual DNA Conformations Are Recognized by Nucleotide Excision Repair

“…Actinomycin D intercalates at G⅐C pairs, and it reduces the number of negative superhelical turns and stabilizes DNA in the right-handed duplex B-form (45)(46)(47)(48)(49)(50). Due to its G-C richness, the poly(R⅐Y) tract offers numerous binding sites for the drug, whose activity is expected to decrease the number of inviable cells.…”