AFM analysis of protamine-induced compaction in short-length DNA fragments

During spermatogenesis, small, positively charged protamine proteins dramatically condense the DNA in the nucleus. This tight compaction both minimizes hydrodynamic drag on the sperm and protects the DNA from ultraviolet radiation. Protamine also is an excellent candidate for use in nanoengineering as a way to self-assemble DNA nanostructures. Here our goal is elucidate the physical mechanism for how protamine causes DNA to fold into a ring of ~50 nm in diameter. To study this question, we used an atomic force microscope (AFM) to image protamine-DNA complexes. By varying the concentration of protamine in the assay, we are able to image the intermediate steps in the folding pathway. We find that short-length (50 nm or less) DNA fragments form half loops that become increasingly more folded as the protamine concentration is increased. Future work will investigate whether this looping is induced by enthalpic or entropic forces.