SEQUENCE-DEPENDENT EXTRUSION OF A SMALL DNA HAIRPIN AT THE N4 VIRION RNA-POLYMERASE PROMOTERS

Bacteriophage N4 virion RNA polymerase promoters contain five to seven -base inverted repeats separated by three bases and centered at positi on -12 from the site of transcription initiation. We have previously s hown that these inverted repeats extrude as hairpins at physiological superhelical densities in a Mg(II)-dependent manner. Mg(II)-dependent hairpin extrusion at promoters P1 and P2 displays quantitative differe nces in reactivity to structural probes at different DNA superhelical densities, with extrusion at P2 being more favored at low superhelical density. Analyses of mutant promoters using structure-specific probes revealed that specific sequences, at the closing base-pair of the hai rpin and at the loop (i.e. 5'-C-GXA-G-3' where X = G, A, T), are requi red for extrusion of the small promoter hairpins at physiological supe rhelical density. The sequence-dependent requirements for extrusion of the small N4 promoter hairpins may be generally applicable for other such sequences found both in prokaryotic and eukaryotic genomes. (C) 1 998 Academic Press.