Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study

Action at a distance: DNA-looping and initiation of transcription

Effective initiation of transcription, especially in eukaryotes, requires the specific assembly of large protein complexes at promoters. We ask here how activator proteins that are bound hundreds or thousands of base pairs away from the promoter might facilitate this process if protein-protein interactions occur via looping of the intervening DNA. We show that the local concentration at the promoter of activator proteins bound at vicinal DNA sites can be substantially regulated by intrinsic or protein-induced distortion of the regular DNA conformation.

Modeling superhelical DNA: recent analytical and dynamic approaches

During the past year, a variety of diverse and complementary approaches have been presented for modeling superhelical DNA, offering new physical and biological insights into fundamental functional processes of DNA. Analytical approaches have probed deeper into the effects of entropy and thermal fluctuations on DNA structure and on various topological constraints induced by DNA-binding proteins. In tandem, new kinetic approaches--by molecular, Langevin and Brownian dynamics, as well as extensions of elastic-rod theory--have begun to offer dynamic information associated with supercoiling. Such dynamic approaches, along with other equilibrium studies, are refining the basic elastic-rod and polymer framework and incorporating more realistic treatments of salt and sequence-specific features. These collective advances in modeling large DNA molecules, in concert with technological innovations, are pointing to an exciting interplay between theory and experiment on the horizon.