With the dawn of nanotechnology, DNA is frequently used as engineering material for constructing various nanomachines. Many such creations rely on DNA strands undergoing a process called DNA Toehold Exchange, where short dangles on DNA Complexes form toeholds allowing target DNA strands to efficiently bind and displace the original strands. However, the kinetics of this process are still not fully understood, requiring much expensive trial-and-error and experimental fitting of rate constants when designing such systems. As such, the goal of research in this area is to better understand the factors influencing the kinetics of this process to reduce the design costs.

In this talk, I will first introduce the DNA Toehold Exchange process and explain the importance of the rate of toehold binding. Then I will introduce the simulation approaches used to derive the rate constants for this process and the sequence factors that we have found to have effects on the rate. Finally, I will discuss limitations of the simulation approaches and possible directions for future research.