Analysis of DNA-RecA protein interactions involving the protein self-association reaction

A method to analyze the DNA binding properties of RecA protein is developed to take into account the protein self-association reaction and is applied to reanalyze the interaction with chemically modified single-stranded DNA (epsilon-DNA). Protein oligomerization is investigated by static light-scattering measurements and analyzed with the accumulated strain model. A coupled equilibrium between DNA binding and self-association of RecA is resolved considering that the complex formed between an m polymer (where m represents the number of units of the polymer) and DNA is identical to the complex resulting from the cooperative binding of m monomers. The cooperativity parameter thus determined is about 10(4), which is more than 100 times higher than the apparent parameter estimated without consideration of the protein oligomerization. This extremely high figure is in good agreement with the formation of large clusters of complex observed by electron microscopy. The apparent DNA binding constant depends upon the ratio of the DNA binding affinity and the self-association constant. For this reason, the variation of the DNA binding constant with the salt concentration is amplified, and the number of ion pairs formed between DNA and RecA obtained from the apparent salt dependence (11 ion pairs/monomer) has been overestimated. Only 2 ion pairs may be formed.