Macro-Molecular Crowding Favors Writhe in Unwound Dna

ABSTRACT Genomic DNA is subject to forces and torsion. Some arise mechanically, while others can be entropic, such as those due to crowding within the nuclear environment. Indeed, about 30-40% of the cell is occupied by molecules other than water, and of these, the vast majority are macromolecules. Here, we explore both experimentally and theoretically the interplay between tension, torsion, and macromolecular crowding. Using pharmaceutically relevant crowders of different molecular weights, Dextran 70, and polyethylene glycol (PEG), we observed that macromolecular crowding of unwound, stretched DNA effectively opposed the tension and promoted the formation of plectonemes. A theoretical model representing the equilibrium between B - and L -form DNA fit to the experimental measurements indicates the contractile tension produced by macromolecular crowding of DNA. SIGNIFICANCE STATEMENT Distinct DNA conformers are involved in different cellular processes. Genomic DNA is both stretched and unwound by enzymes in a crowded intracellular medium. This can induce conformational changes between extended, twisted and more compact, plectonemic forms. This study explores the effect of macro-molecular crowding on the conformations of DNA subject to tension and torque. Fitting experimental data to a model for the right-to-left-handed DNA transition, we show that macromolecular crowding induces a contractile force that favors DNA writhe and that such force depends both on the concentration and molecular weight of the crowder.