Figure 4.

J factors decrease as DNA tethers shorten especially when the DNA becomes negative supercoiled. (A) Increasing the HU concentration surrounding Os-400-O1 (diamonds) or O1-400-O2 (upright triangles) tethers drives the J factors to saturation at multiples of 11–15. Slight tension lowered the HU-improved J factors back toward their original values (left and right-pointing triangles). (B) The J factor measured for O1-400-O2 in TPM experiments (with negligible tension) was 4 nM (cyan star). Slight tension precluded looping (J << [LacI] = 1 nM) until the DNA became sufficiently supercoiled (Figure 1B). Indeed, supercoiling, especially negative, increased J factors by several orders of magnitude to levels (J>> [LacI] = 1 nM) beyond that reported for a 400 bp loop in vivo (purple dashed line).