DNA packaging and polycation length determine DNA susceptibility to free radical damage in condensed DNA

In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins; histone in somatic nuclei and protamines in sperm chromatin. The extreme, near-crystalline packaging of DNA by protamines in spermatozoa is thought essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species. The protective role of protamine is required in sperm as they are sensitive to ROS damage due to the progressive loss of DNA repair mechanisms during maturation. The degree to how DNA packaging directly relates to DNA protection in the condensed state, however, is poorly understood. Here, we utilized different polycation condensing agents to achieve varying DNA packaging densities and quantify DNA damage by free radical oxidation within the condensates. Although we see that tighter DNA packaging generally leads to better protection, the length of the polycation also plays a significant role. Molecular dynamics simulations suggest that longer polyarginine chains offer increased protection by occupying more space on the DNA surface and forming more stable interactions. Taken together, our results suggest a complex interplay between polycation properties, DNA packaging density, and DNA protection against free radical damage within condensed states.