The surprising ways in which macromolecular crowders affect DNA structure and topology

Cells are crowded by several macro-molecules. Crowding gives rise to entropic forces that change both inter- and intra-molecular interactions. Using single molecule approaches, we show that macromolecular crowders, such as PEG and Dextran, which are often used in medical/pharma applications, (1) stabilize the right-handed structure of DNA against unwinding, (2) favor the parallel (solenoidal) vs. anti-parallel conformation of commonly sized protein-mediated DNA loops and (3) decrease the persistence length of DNA facilitating compaction. Therefore, changes in macromolecular crowding may significantly affect genomic structure and function and induce different chromatin/genomic phases. We used magnetic, or optical, tweezers to manipulate single DNA molecules, probe their compaction and torsional state in the presence of crowders and, eventually, test models of crowding effects. A numerical approach to solving the tadpole model of a polymer under tension reproduced data on DNA compaction as a function of crowder volume fraction and/or pulling tension. Assuming that crowders effectively increase the osmotic pressure on the DNA polymer mesh as found in a semi-dilute solution or in supercoiled DNA, scaling relations well simulate the effect of unwinding DNA under tension. These examples illustrate the power of combining experimentation with theoretical modeling to probe the effects of crowding on the genome.