RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template

RNAs bind directly to Pol II and prevent the binding of Pol II to an open DNA complex. (A) Binding of Pol II to a pre-tRNA^Tyr transcript. A constant amount of α-³²P pre-tRNA^Tyr was incubated with titrated amounts of purified yeast Pol II and separated on a 5% native polyacrylamide gel. (B) Inhibition by RNA of Pol II-DNA complex formation. Indicated amounts of tRNA^Tyr were incubated with a constant amount of Pol II (30 nM) for 15 min at 30°C. These Pol II-RNA complexes were then incubated with the CKO432-CKO433 preformed open DNA complex for 15 min to a final volume of 10 µL. Complexes were separated on a 5% native gel. The Pol II-DNA band separated from free DNA. (C) The reaction in B was repeated in triplicate for four different RNAs. Total radioactive signal per lane was quantitated and plotted.