Effects of macromolecular crowding on the collapse of biopolymers

Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment

We investigate the conformations of DNA-like stiff chains, characterized by contour length (L) and persistence length (lp), in a variety of crowded environments containing monodisperse soft spherical (SS) and spherocylindrical (SC) particles, a mixture of SS and SC, and a milieu mimicking the composition of proteins in the Escherichia coli cytoplasm. The stiff chain, whose size modestly increases in SS crowders up to ϕ ≈ 0.1, is considerably more compact at low volume fractions (ϕ ≤ 0.2) in monodisperse SC particles than in a medium containing SS particles. A 1:1 mixture of SS and SC crowders induces greater chain compaction than the pure SS or SC crowders at the same ϕ, with the effect being highly nonadditive. We also discover a counterintuitive result that the polydisperse crowding environment, mimicking the composition of a cell lysate, swells the DNA-like polymer, which is in stark contrast to the size reduction of flexible polymers in the same milieu. Trapping of the stiff chain in a fluctuating tube-like environment created by large-sized crowders explains the dramatic increase in size and persistence length of the stiff chain. In the polydisperse medium, mimicking the cellular environment, the size of the DNA (or related RNA) is determined by L/lp. At low L/lp, the size of the polymer is unaffected, whereas there is a dramatic swelling at an intermediate value of L/lp. We use these results to provide insights into recent experiments on crowding effects on RNA and also make testable predictions.

Concentrating genomic length DNA in a microfabricated array

We demonstrate that a microfabricated bump array can concentrate genomic-length DNA molecules efficiently at continuous, high flow velocities, up to 40 μm/s, if the single-molecule DNA globule has a sufficiently large shear modulus. Increase in the shear modulus is accomplished by compacting the DNA molecules to minimal coil size using polyethylene glycol (PEG) derived depletion forces. We map out the sweet spot, where concentration occurs, as a function of PEG concentration and flow speed using a combination of theoretical analysis and experiment. Purification of DNA from enzymatic reactions for next-generation DNA-sequencing libraries will be an important application of this development.

Unusual domain movement in a multidomain protein in the presence of macromolecular crowders

FRET-based distance changes between domains I and II of HSA reveal significant differences in the manner in which dextran based macromolecular crowding agents influence the serum protein.