Daunomycin modifies the sequence-selective recognition of DNA by actinomycin

The theory of interceptor-protector action of DNA binding drugs

The review discusses the theory of interceptor-protector action (the IPA theory) as the new self-consistent biophysical theory establishing a quantitative interrelation between parameters measured in independent physico-chemical experiment and in vitro biological experiment for the class of DNA binding drugs. The elements of the theory provide complete algorithm of analysis, which may potentially be applied to any system of DNA targeting aromatic drugs. Such analytical schemes, apart from extension of current scientific knowledge, are important in the context of rational drug design for managing drug's response by changing the physico-chemical parameters of molecular complexation.

Elasticity as the Basis of Allostery in DNA

Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here, we show that trends in the interaction energy of ligands binding to DNA can be explained within an elastic birod model, which accounts for the deformation of each strand as well as the change in stacking energy due to perturbations in position and orientation of the bases caused by the binding of ligands. The strain fields produced by the ligands decay with distance from the binding site. The interaction energy of two ligands decays exponentially with the distance between them and oscillates with the periodicity of the double helix in quantitative agreement with experimental measurements. The trend in the computed interaction energy is similar to that in the perturbation of groove width produced by the binding of a single ligand, which is consistent with molecular simulations. Our analysis provides a new framework to understand allosteric interactions in DNA and can be extended to other rod-like macromolecules whose elasticity plays a role in biological functions.

Altered cleavage of DNA sequences by bleomycin and its deglycosylated derivative in the presence of actinomycin

The antitumour antibiotics bleomycin and actinomycin are commonly used therapeutically in combination. One causes metal ion- and oxygen-dependent oxidative damage to DNA, while the other acts at the level of DNA via intercalation of its phenoxazone chromophore and probable inhibition of topoisomerases. Both drugs bind and/or cleave DNA primarily at guanine-containing sequences, which could lead to mutual interference. Using three different restriction fragments we show that binding of actinomycin to DNA causes major alterations in the sequence specificity of bleomycin.Fe-mediated cleavage, including the appearance of new cleavage sites and the suppression of others. The subtle sequence-dependence of the interference is illustrated by the different effects of actinomycin on DNA cleavage by the deglycobleomycin.Fe complex. Actinomycin sharply decreases the extent of cleavage at GpC sites by both bleomycin and deglycobleomycin whereas cleavage at GpT sites is much less affected, while novel cleavage sites are generated at GpA, ApT and, to a lesser extent, TpT steps. A dramatic increase in bleomycin.Fe cutting at GpA is barely detectable with deglycobleomycin.Fe, confirming that the carbohydrate moiety of bleomycin is important for DNA recognition. The results contribute to a better understanding of how two individually well-characterized small molecules interact simultaneoulsy with specific sequences in DNA and as such assist clarification of the principles governing drug-DNA recognition.

Sequence-selective intercalation of antitumour bis-naphthalimides into DNA. Evidence for an approach via the major groove

LU 79553, a bis-naphthalimide drug highly active against human solid tumour xenografts, has been shown to bis-intercalate into DNA with a helix-unwinding angle of 37 degrees. Footprinting experiments with DNase I reveal that the drug is selective for mixed nucleotide sequences characterised by an alternating purine-pyrimidine motif, particularly those containing GpT (ApC) and TpG (CpA) steps. Derivatives bearing nitro or amino substituents on the naphthalimide chromophores bind at essentially identical sites. The footprinting profiles on tyrT DNA and on two fragments from pBS bear a remarkable resemblance to those determined for nogalamycin, an antibiotic which binds intercalatively leaving bulky carbohydrate substituents blocking both the major and minor grooves of the helix. Several lines of evidence indicate that the bis-naphthalimides recognise their preferred binding sites via the unusual expedient of intercalating from the major groove. Footprints on the complementary DNA strands sometimes appear staggered in the 5'direction. Repositioning the 2-amino group of G.C base pairs, which serves as a critical minor-groove marker, by substitution with inosine and/or 2,6-diaminopurine has little effect on the distribution of binding sites for LU 79553. The bis-naphthalimides affect the guanine-specific reaction with dimethyl sulfate (which reacts with the N7 position of the base located in the major groove) but not reactions with tetrachloropalladinate or methylene blue. Photoactivation of LU 79553-DNA complexes leads to a small amount of strand scission mainly at guanine residues. These observations make a strong case for binding via the major groove of the double helix, in contrast to nearly all common intercalating drugs, which could be important in explaining the unique biological selectivity of bis-naphthalimides.

Analogue versus digital recognition of DNA by bleomycin: an effect of the carbohydrate moiety

We have sought to determine the influence of the carbohydrate moiety of the antitumour antibiotic bleomycin on the sequence-specific cleavage of DNA. Both bleomycin A2 and deglycobleomycin A2 produce different cleavage patterns with DNA in which the 2-amino group has been removed from guanine, added to adenine, or both, as well as on a designed DNA fragment containing a few defined cleavage sites. Although each drug cleaves DNA primarily at GpT and GpC sites, the cleavage at these sites is frequently found to be stronger with deglycobleomycin compared with bleomycin A2. Conversely, in most cases the cleavage at secondary sites, in particular at ApT steps, is significantly reduced or even abolished with deglycobleomycin. The results indicate that the gulose-mannose moiety of bleomycin A2 plays a significant role in the recognition of preferred nucleotide sequences and confirm the view that both secondary structure and interaction with guanine are involved in determining sequence-specific cleavage of DNA by bleomycin.