It is common for sing1e-stranded nucleic acid finding proteins to bind polynucleotides cooperatively. The parameter ω is used to describe the component of the association binding constant that is due to cooperative interactions between protein molecules on the polynucleotide lattice; ω is 1 for noncooperative binding, while ω can be as high as 103-104 for highly cooperative proteins such as bacteriophage T4 gene 32 protein. In the past, to has been determined by computer fitting of spectroscopic titration data. It has been suggested that electrom microscopy would provide a more direct method for estimation of the cooperativity parameter. An equation can be derived that relates the experimentally obtained average protein cluster size (at a specific protein/RNA saturation ratio) to ω. The only other parameter required for the calculation is the RNA binding site size obtained from stoichiometric titration measurements.
DNA "melting" proteins. II. Effects of bacteriophage T4 gene 32-protein binding on the conformation and stability of nucleic acid structures.
