Yannan Shen

Mathematical analysis of DNA unknotting by type II topiosomerases

Type II topoisomerases are enzymes that can change the topology of circular DNA molecules. These enzymes are essential to every living organism, which makes them good targets for anti-cancer and anti-bacterial drugs. DNA topology assays are used to determine the efficiency of topoisomerase inhibitors in drug design. In my research, I focus on the unknotting probability of knots by type II topoisomerases. In our previous study, our group built a mathematical model in simple cubic lattice to simulate how random strand passages generate the knotting distribution. We intended to use a sophisticated theoretical framework and efficient computer simulations to test and compare some of the existing models and propose new ones. I aim to implement the random strand-passage model in the Dowker code level to discover how topo II simplifies knots under the thermal dynamic equilibrium level.

Message to Sponsor

As a transfer student, I came to Berkeley last fall and felt research was something impossible for me to do. One year later, with the help from the SURF award, I was able to explore a project myself and for the first time realize how useful my major mathematics is. As I was working on my project, I also realized how important everything I have learned in class was. For example, R language helped me a lot with data analysis. In fact, I learned it just for fun and I was never expecting to use it again. I am really glad I was given the opportunity to apply my knowledge to a project that I am interested in. I am also thankful for my mentors, who are knowledgeable and so patient to guide me throughout my research progress.
  • Major: Mathematics
  • Mentor: Rainer Sachs, Mathematics