DNA Bendability—;A Novel Feature inE. coliPromoter Recognition

The distribution of deformable base-pair steps in the structure of bacterial promoters is analyzed with respect to their possible structural and functional role. A regular positioning of TA and TG stacks is detected with the best fit period 5.6 bp. This value is interpreted as a half of the sequence period 11.2 bp, somewhat higher than the structural helical repeat of B-DNA (10.55 bp). The difference, +0.65 bp, suggests a sequence-dependent helical writhe of the promoter DNA--a right-handed superhelix. Apparently, to favour rotational setting of DNA on the surface of RNA polymerase the flexible steps deformable largely towards the grooves, follow the half-period spacing. Such rotational setting is consistent with the DNase I footprinting data. Periodical distribution of deformable base-pair stacks shows negative correlation with the presence of -35 canonical hexamer, suggesting the functional significance of this novel element for promoter recognition. The RNA polymerase--DNA recognition is discussed as interaction of distributional type that involves many elements of different nature which are in partially compensatory relations.