Supercoiling and Looping Promote DNA Base Accessibility and Coordination among Distant Sites

Abstract

Despite the importance and ubiquity of DNA supercoiling, relatively little is known about how supercoiling modulates DNA structure and its interactions with proteins and other biological molecules. To begin to address this shortfall, we studied the 3-D structures of individual 336 bp DNA minicircles over a wide range of supercoiling—from positive to hyper-negative—using electron cryotomography. Supercoiled minicircles contort into a surprisingly wide variety of conformations, many of them containing sharp bends, even though DNA is rigid and should be resistant to bending.