Computational analysis of looping of a large family of highly bent DNA by LacI.

ABSTRACT: Sequence-dependent intrinsic curvature of DNA influences looping by regulatory proteins such as LacI and NtrC. Curvature can enhance stability and control shape, as observed in LacI loops formed with three designed sequences with operators bracketing an A-tract bend. We explore geometric, topological, and energetic effects of curvature with an analysis of a family of highly bent sequences, using the elastic rod model from previous work. A unifying straight-helical-straight representation uses two phasing parameters to describe sequences composed of two straight segments that flank a common helically supercoiled segment. We exercise the rod model over this two-dimensional space of phasing parameters to evaluate looping behaviors. This design space is found to comprise two subspaces that pre

SUBMITTER: Lillian TD 

PROVIDER: S-EPMC2599832 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature