(250a) DNA Looping Mediated by Two-Site Binding Proteins: Insights From Brownian Dynamics Simulations

The formation of loops in DNA, i.e., distant sites on a DNA strand being in close proximity of each other play cellular regulatory roles in prokaryotes and eukaryotes. Moreover, looping can be modulated by two-site binding proteins that bind genomically distant sites and stabilize the DNA substrate thus facilitating the participation of other cellular machinery (e.g., transcription factors). Loop formation induced by binding proteins and its local stabilizing effects on DNA are presumed to be a key regulatory mechanism in vitro. As an example, the protein p53 (the ``Master Watchman'' protein) is known to, halt cell growth, assist in tumor suppression and trigger apoptosis. Understanding the physics of looping, modulated by binding proteins, is then crucial to inferring to the physical mechanisms used by proteins such as p53. Moreover, recent optical tweezer experiments on the forced induced disruption of two-site restriction endonucleases by Smith et al. show that a complex force extension relationship exists for even the simplest binding proteins. In this work we present a coarse grained model of the DNA looping phenomena using Brownian dynamics simulations. We model the DNA strand as a Worm Like Chain (WLC) and include a two-site binding protein in the model. We show that DNA looping in the absence of binding proteins occurs with a natural length scale of less than 500bp in the context of the WLC model. We provide a detailed analysis from the BD simulations of the effects of looping induced by two-site binding proteins, including effects of; i) protein size, ii) protein binding site morphology, iii) DNA stiffness and iv) DNA length on the resultant loops that form. We discuss how such simulations can help to interpret DNA looping experiments and provide insight into the energy landscape of binding proteins. We suggest extensions of our work which can be used to model the more physically relevant situation of binding proteins operating in the complicated milieu of chromatin.