Characterizing Protamine-Induced DNA Loop Formation Using a Tethered Particle Motion Assay

Protamine is a protein found in sperm cells. It folds DNA into compact toroids by first forming it into loops and then stacking those loops. This compaction plays an important role in reproduction, ensuring that sperm are hydrodynamically efficient and protecting the DNA they carry. We use a tethered particle motion assay to examine the mechanics of loop formation in this process. By tracking the Brownian motion of a bead tethered to a length of DNA, we can detect changes in DNA conformation through changes in the bead's motion. We find that loop formation is a multi-step process with intermediate states.