No abstract

DNA compaction in a bacterial cell is in part carried out by entropic (depletion) forces induced by "free" proteins or crowding particles in the cytoplasm. Indeed, recent in vitro experiments highlight these effects by showing that they alone can condense the E. coli chromosome to its in vivo size. Using molecular dynamics simulations and a theoretical approach, we study how a flexible chain molecule can be compacted by crowding particles with variable sizes in a (cell-like) cylindrical space. Our results show that with smaller crowding agents the compaction occurs at a lower volume fraction but at a larger concentration such that doubling their size is equivalent to increasing their concentration fourfold. Similarly, the effect of polydispersity can be correctly mimicked by adjusting the size of crowders in a homogeneous system. Under different conditions, however, crowding particles can induce chain adsorption onto the cylinder wall, stretching the chain, which would otherwise remain condensed.

We study the relationship between intrachain ordering and segregation tendency of two polymers confined in a cylindrical space. We find the chains segregate spontaneously even outside de Gennes' linear-ordering scaling regime, in which each chain is a linear array of blobs. When the chains are weakly compressed against each other, linear ordering is well preserved and the chains remain segregated. On the other hand, for moderate compression, new chain-ordering units emerge at intermediate length scales, within which blobs are randomly packed; yet these units (termed "superblobs") are linearly ordered, and the chains still segregate in the confined space. As the chains continue to be compressed, the linear regime disappears, but the chains can resist mixing effectively, more so in a more asymmetric space. We conclude that the linearly ordered E. coli chromosome is in the segregation regime.