Student: Aaron Kirchman, Undergraduate Student in Physics and Mathematics, University of Northern Iowa
Research Mentor: Dr. Ali Tabei
Stochastic Monte Carlo Simulations of Competing Nucleoproteins on Single-Stranded DNA
A crucial step in the DNA repair mechanism of homologous recombination is the search for homology between DNA molecules. This step is quickly followed by strand exchange between homologous DNA. This step is governed by the nucleoprotein RAD51 which competes with Replication Protein A (RPA) to saturate single-stranded DNA (ssDNA) overhangs. These interactions are stochastic in nature. Therefore, a dynamic stochastic model is the best representation of the real molecular process occurring during homologous recombination. Forming a stochastic Monte Carlo model of the competition between RAD51 and RPA allows for the observation of real-time dynamics during these interactions. Such a dynamic model was developed in MATLAB and is being used to study the effects that various governing parameters have on each protein’s saturation level on ssDNA.