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The intercalation model of DNA–hydrocarbon binding appears reasonable, but rests on indirect evidence only. To test the model, a size criterion for binding has been proposed. The size criterion is based on the assumption that hydrophobic forces play a major role in the binding of hydrocarbons to DNA. It states that hydrocarbons which are small enough to intercalate into DNA and be well protected from contact with the medium, will be found to bind to DNA; those that are too large will not. We report results on the binding of fourteen polycyclic aromatic hydrocarbons to DNA. Predictions based on the size criterion were found to be valid in all cases tested.

A number of polycyclic aromatic hydrocarbons bind to the double-stranded, acid form of polyadenylic acid (poly A). Model building shows that these hydrocarbons may intercalate in the helix, and be well protected from contact with the aqueous medium. Hydrocarbons that are too large to be so protected are found not to bind. A size criterion for the binding of hydrocarbons to poly A therefore exists. This criterion differs from one that was previously found for DNA. The size criteria for DNA and poly A, together, serve as strong evidence for the intercalation model for hydrocarbon complexes. Model-building experiments show that only a small portion of the hydrocarbon need extend into the medium to prevent binding. This finding implies that in two cases (1,2,5,6-dibenzanthracene·poly A and 3,4-benzpyrene·DNA) the structure of the complex is almost completely determined by the size criterion alone.

Ultraviolet absorption, fluorescence excitation and emission, and fluorescence anisotropy demonstrate that the polycyclic aromatic hydrocarbone 3,4-benzpyrene, Pyrene, anthracene, and 9-methylanthracene bind to histone IV after the sow conformational change in the presence of divalent phosphate anion. These hydrocarbons do not bind, within our limits of detection, to histone IV in the diosorderde form at low pH or to the form produced by the fast conformational change when the slow change is prevented. High anisotropy values for the bound hydrocarbon indicate a high degree of aggregation for the histone IV.