Binding of the recA protein of Escherichia coli to single- and double-stranded DNA

The recA protein of Escherichia coli binds both single- (SS) and double-stranded (DS) DNA; however, the optimal conditions differ for interaction with these DNA substrates. Binding of DS DNA by recA protein is pH dependent (optimum near pH 6.2) and requires a nucleoside triphosphate (ATP) and divalent cation. Substitution of the 5'-O-3'-thiotriphosphate (ATP(gamma S)) for ATP leads to formation of stable complexes of recA protein and DNA that dissociate very slowly. Formation of these complexes is extremely sensitive to ionic strength and pH. However, once formed, the complexes resist changes in pH and high salt concentrations. SS DNA binds to recA protein in the absence of a nucleoside triphosphate, but recA protein-SS DNA complexes are stabilized by ATP(gamma S). At high recA protein/DNA ratios (1 recA protein monomer/30 nucleotides), these complexes sediment in sucrose gradients as large protein-DNA aggregates. Although ATP(gamma S) blocks dissociation of recA protein from DNA, ATP stimulates the release of recA protein from SS DNA. Hydrolysis of the ATP is not required for dissociation since it is also enhanced by ADP and certain nucleoside triphosphates that are not hydrolyzed by recA protein. recA protein binds with different affinities to ribohomopolymers and deoxyhomopolymers. It preferentially binds polydeoxythymidylate and polydeoxycytidylate but does not bind short oligonucleotides, indicating that there is a minimum size requirement for the binding step. The recA protein exists as a heterogeneous aggregate at pH 7.5 and at low ionic strength. At pH 6.2 in the presence of Mg2+, the protein sediments homogeneously as a dimer. At pH 6.2, ATP or ATP(gamma S) promotes an oligomerization of the recA protein which can be observed as filamentous structures by electron microscopy. Oligomerization is not induced by UTP, a nucleoside triphosphate that is efficiently hydrolyzed by the recA protein, but fails to stimulate efficiently recA protein-promoted annealing and assimilation of single-stranded DNA.