The proposed research is designed to obtain a molecular understanding of the interactions of the E. coli Single Strand Binding (SSB) protein with single stranded (ss) nucleic acids, using thermodynamic, kinetic, biochemical and structural approaches. The SSB protein is a helix-destabilizing protein, which binds selectively and cooperatively to ss nucleic acids. It is an essential protein in E. coli, which is required for DNA replication and is involved in a variety of recombination and repair processes in vivo. The E. coli SSB tetramer has recently been shown to bind to ss nucleic acids in a number of different modes, depending on the solution conditions, each possessing different site sizes. This reflects, in part, the different degrees of DNA wrapping about the tetramer. It also binds to ss polynucleotides with at least two different types of positive cooperativity between tetramers, yet it is not clear which of these modes or cooperativities is used by the SSB protein in its various functions. The applicant's intent is to understand the binding properties of the SSB protein and the structures of the complexes in the different modes. Effects of solution conditions on the stability of the different complexes and the transitions among the binding modes in vitro are of particular interest. The binding of the SSB protein to ss nucleic acids in each of these binding modes will be characterized by determining the equilibrium binding parameters (affinity and positive cooperativity). These binding parameters will be obtained as a function of solution variables (salt concentration and type, temperature and pH) in order to understand the thermodynamic basis for the stability of each mode, as well
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