Indications of a more complex DNA toroid formation.

Abstract

The compaction of DNA in sperm is at semi-crystalline levels, reaching nearly the physical condensation limit. This incredible compaction is carried out by a positively charged condensing agent, the protein protamine. Many protamines bind to the negatively charged DNA backbone, each creating a bend that eventually forms a loop. Our goal is to determine how protamine compacts the DNA even further to form toroids. Using atomic force microscopy (AFM), we imaged samples of varying lengths of DNA (1-48 kbp) under varying concentrations of protamine (0.1-3 μM). This allowed us to isolate folding states in the toroid formation pathway. It is thought that toroids are formed loop by loop and create a hexagonally packed toroid. However, we observed structures with many unstacked loops that look like flowers, vertical stacks of several loops, rod-like structures with approximately the thickness of a toroid, and toroids with nonuniform diameter and height. These structures suggest that the DNA toroid formation pathway could be more complex than we first thought. Could there be multiple pathways for the formation of toroids? Here we will present our progress toward determining toroid formation mechanisms. Understanding the physics of DNA compaction into a toroid may have interesting nanoengineering applications.