A complementary DNA oligomer releases a transcription pause complex

Abstract

The formation of alternative secondary structures in the transcript of the tryptophan (trp) operon leader region regulates expression of the trp operons of Escherichia coli and other bacterial species. During in vitro transcription RNA polymerase pauses near base pair 90 after the first hairpin secondary structure in E. coli trp leader mRNA is formed. The E. coli L-factor enhances transcription pausing at this site (Farnham, P. J., Greenblatt, J., and Platt, T. (1982) Cell 29, 945-951); presumably it does so by facilitating recognition of the RNA hairpin by polymerase. We show that addition of a DNA oligomer complementary to the proximal segment of the RNA hairpin relieves transcription pausing in vitro both in the presence and absence of L-factor. The oligomer apparently interferes with formation of the RNA hairpin which we believe is recognized by polymerase as the pause signal. The oligomer also relieves pausing in L-factor-induced paused complexes, suggesting that the oligomer can disrupt a preformed secondary structure in the transcript.