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 Qβ 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 Qβ 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 Qβ RNA is proposed to result from the binding of an aggregate, which can interact with several low affinity sites on the RNA simultaneously.
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