The binding of protamines to DNA; role of protamine phosphorylation

The thermodynamics of protamine-DNA interation was investigated with clupeine Z from herring labeled at its amino terminus with fluorescein. The ionic strength dependence, the influence of protamine phosphorylation, of the native DNA conformation, using native and heat-denatured DNA, and of the protamine primary structure, using two oligoarginine peptides of similar length as the clupeine, was thoroughly studied. The unusually high cooperativity of interaction found is strictly correlated to the native DNA conformation and the protamine primary structure. Cooperativity is explained by cross-linking of DNA segments resulting in an increase of the negative charge density. The importance of protamine phosphorylation lies in the fact that thermodynamically governed interaction with DNA and favorable cross-linking of DNA are shifted to physiologically reasonable ionic strengths.