Self-Assembly of the Catalytic Formation of Three-Arm Junctions in DNA

Self-Assembly is the process by which individual parts spontaneously rearrange into a desired structure.  This process is commonly seen in chemical reactions and is very important for many biological phenomena.  The specific occurrence that we are focusing on is the catalytic formation of three-arm junctions of DNA strands.  We created a simulation for the above reaction using conditional programming in Matlab.  Our simulation consists of constituent particles that move randomly within a bounded rectangular area. Each particle represents a metastable monomer and follows a set of rules. When two particles collide, they can either bind or bounce off of each other.  The outcome of this collision is determined by predefined rules and an adjustable probability of binding.  The probability represents the concentration of the catalyst that would be used in the actual experiment.  We included a malfunctioning particle to evaluate how this would affect the process. We then measure the time-complexities and the reaction rates of our simulation with and without the malfunctioning particle. Our resulting graphs share many characteristics with the experimental graphs. Besides providing a symbolic visualization of a chemical procedure, our simulation allows scientists to analyze the catalytic formation of three-arm DNA junctions more rapidly and without the expensive materials.