A gel-concentration-independent retardation detected in two fragments of the rrnB P1 promoter of E. coli using transverse polyacrylamide pore gradient gel electrophoresis.

Two fragments of the E. coli rrnB ribosomal RNA P1 promoter Upstream Activation Region exhibit a constant gel retardation, over a polyacrylamide gel concentration range of 3% to 10%. Gel retardation is usually seen to increase with polyacrylamide gel concentration as in the case of the 219 base pair Crithidia fasciculata kinetoplast DNA fragment which represents the classic case of sequence directed curvature. Computer modeling of the Upstream Activation Region fragments suggests that their unusual electrophoretic behavior can be accounted for on the basis of a "screw" model proposed by Drak and Crothers (1991, Proc. Natl. Acad. Sci. USA 88,3074-3078).