Unexpected swelling of stiff DNA in a polydisperse crowded environment

TL;DR

This study reveals that stiff DNA-like chains unexpectedly swell in complex, polydisperse crowded environments, contrasting with flexible polymers, due to trapping in fluctuating tube-like regions created by large crowders.

Contribution

It uncovers the counter-intuitive swelling of stiff DNA in polydisperse crowded environments, providing new insights into cellular crowding effects on biopolymers.

Findings

Stiff DNA modestly increases in size with soft spherical crowders at low volume fractions.

DNA becomes more compact in monodisperse spherocylindrical crowders than in spherical ones.

Polydisperse crowders cause DNA swelling, contrasting with flexible polymer behavior.

Abstract

We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC) particles, mixture of SS and SC, and a milieu mimicking the composition of proteins in $E. coli.$ cytoplasm. The stiff chain, whose size modestly increases in SS crowders up to $\phi\approx 0.1$, is considerably more compact at low volume fractions ($\phi \leq 0.2$) 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 $\phi$ with the effect being highly non-additive. We also discover a counter-intuitive result that 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 polymer 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 $L/l_p$. At low $L/l_p$ the size of the polymer is unaffected whereas there is a dramatic swelling at intermediate value of $L/l_p$. We use these results to provide insights into recent experiments on crowding effects on RNA, and also make testable predictions.