Studies of the binding of actinomycin and related compounds to DNA.

Equilibrium, kinetic and hydrodynamic studies are reported of the binding to DNA of actinomycin, its derivatives, and some simpler analogs. The major conclusions are: (1) The actinomycin chromophore is intercalated between the base pairs in the DNA complex. (2) Binding can occur adjacent to any GC pair, but binding at a given site produces a distortion of the helix that greatly disfavors binding of another actinomycin closer than six base pairs away. (3) The source of the helix distortion is probably a pair of hydrogen bonds formed between the deoxyribose ring oxygens and the -CONH- groups attached to the chromophore. (4) The specificity for guanine among the common bases results from electronic interactions in the π-complex formed in an intercalated structure. Studies of complex formation between actinomycin and simple aromatic systems make this conclusion plausible. (5) Several forms of the complex exist at equilibrium; these result from conformational changes within the cyclic peptide rings of actinomycin. (6) In the most stable form of the complex, the peptide rings have undergone conformational changes which adapt their structures to interact specifically with the DNA backbone, one ring interacting with each strand of the double helix. (7) The physical property which distinguishes actinomycin from the simpler analogs (which lack biological activity) is a very slow dissociation reaction, several orders of magnitude slower than for the non-active analogs. The structural basis for the slow dissociation is the slow reversal of the conformational change of the peptide rings. The peptide ring containing five amino acids is probably selected for this function because of the great steric hindrance to conformational changes inherent in such a tightly packed structure.