Interaction of Escherichia coli host factor protein with Q beta ribonucleic acid

The affinity of Escherichia coli host factor protein for a variety of ribonucleic acids (RNAs) is compared in an equilibrium competition assay with (pA)15 or (pA)27 as the common probe. Of the homopolymers tested, only polyriboadenylate [poly(rA)] binds the protein with a high affinity. At low ionic strength (0.1 M NaCl), the binding to Q beta RNA is much stronger than to the oligoadenylates, but the situation is reversed upon fragmentation of the RNA with ribonuclease T1. Increasing the ionic strength results in a drastic reduction of the affinity of host factor for Q beta RNA over a relatively narrow salt range (0.1--0.3 M NaCl). Over the same range, added salt greatly reduces the tendency of host factor hexamers to aggregate. The tight binding of host factor to Q beta RNA is proposed to result from the binding of an aggregate, which can interact with several low affinity sites on the RNA simultaneously.