Stable DNA Loops in Vivo and in Vitro: Roles in Gene Regulation at a Distance and in Biophysical Characterization of DNA

Abstract

Publisher Summary This chapter discusses the quantitative information available regarding action-at-a-distance in a variety of systems (primarily prokaryotic), in which the formation of stable DNA loops has been proposed as the mechanism of the effect. Primarily, this chapter focuses on the use of quantitative studies of the length dependence of action-at-a-distance to investigate the physical properties of DNA in vivo. In addition, it discusses the biophysical basis of two mechanisms proposed to explain regulatory effects of DNA looping: local concentration (direct) effects and topological (indirect) effects. In principle, “action-at-a-distance’’ may be either a “through-space” or a “through-bond’’ effect, in the jargon of two-dimensional NMR spectroscopy. Formation of stable DNA loops (DNA looping), the subject of this review, is a “through space” effect, involving two regions of DNA distant along the contour of the molecule, and one or more proteins that contact these two regions simultaneously via bending and/or curvature of the intervening DNA sequence. Possible “through-bond’’ (along the DNA contour) thermodynamic models for action at a distance have also been considered, including the long-range effects of the changes in DNA secondary structure, induced by changes in supercoiling, as well as long-range cooperativity of protein binding and/or DNA structure.