Physical biochemical studies of a single-stranded nucleic acid binding protein termed A1 were conducted. The protein binds cooperatively to either RNA or DNA and the full length protein binds much tighter than a truncated A1 protein lacking the glycine-rich COOH-terminal domain (residues 185-319). Our studies suggest the mechanism of A1 binding is, in some respects, similar to that of two well-known prokaryotic ssDNA binding proteins: Binding involves charge-charge interactions and close approach of aromatic amino acids to nucleotide bases. Our findings indicate that both the NH2-terminal and COOH-terminal domains of the intact A1 protein make significant contributions to the overall free energy of binding of A1 to nucleic acids. Both the COOH-terminal fragment and intact protein have strand annealing activity for both RNA and ssDNA. This is of particular interest, since the results suggest that A1 could play a role in pre-mRNA splicing and/or homologous DNA recombination.
