Macromolecular Crowding and Nanoscale Confinement on the Structural Regulation of Chromatins/DNAs

Abstract

DNA is a very long polymeric molecule that governs the genetic processes in cells, and its structural regulation is critical to their functions. In addition, several uses of DNA as a novel material have also been proposed in nanomaterial science and engineering. In this account, we introduce our efforts to understand the regulatory strategies of chromatins (a very long DNA molecule complexed with and compacted by a large number of histone protein complexes) in crowded cellular environments and in nanoscale confinements, using computer simulations of chromatins. We first show that macromolecular crowding in the cell nucleus has distinguishable influences on chromatins with different compaction densities, suggesting that cellular control of macromolecular crowding may be utilized to control different chromatin domains, called heterochromatin and euchromatin. Then, we also show that chromatins placed in an array of nanoscale posts have different molecular arrangements depending on the dimension of the nanopost arrays: either localized and aligned parallel to the nanoposts or distributed perpendicular to the nanoposts. Our studies suggest that the entropic effects of macromolecular crowding and nanoscale confinement can regulate chromatin structures and arrangements.