DNA Aggregation and Condensation by Charged Agents

Abstract

While DNA is one of the longest and the stiffest molecules in nature and is negatively charged, it is strongly condensed in a tiny space of cell nuclei and in some virus thanks to polyvalent cations and/or small basic proteins. For example, protamine, a small arginine-rich basic protein plays an important role in packaging paternal genome into sperm nuclei during spermatogenesis, achieving a 106-fold compaction of DNA. In dilute solutions containing various charged condensing agents, short DNA fragments as well as long DNA chains form also aggregates and condensates, some of them being reminiscent of those found in vivo. We present molecular dynamics simulations of DNA aggregation and condensation using a simple idealized model roughly reproducing DNA grooves and incorporating solely long-range electrostatic and steric interactions. The DNA microscopic organization is analyzed and discussed in comparison to 3D high-resolution cryoTEM images.