Non-Uniform spatial distribution of protamine induced DNA looping

In cells, the genome is both regulated and protected by DNA looping. Many studies have focused on the role played in looping by prokaryotic transcription factors like lac repressor or by structural maintenance proteins such as condensin. We are interested in exploring another mechanism, where condensing agents (charge ≥ +3) such as protamine proteins neutralize the DNA and cause it to form loops and toroids. We examine two different proposed mechanisms by which protamine could cause loop formation in DNA.