Olivia Zou
Brandeis / Mathematics, Biological Physics
Hosted by Rogers' Lab
“Exploring the Thermodynamics behind Biomolecular Competition”
Olivia Zou, W. Benjamin Rogers
Abstract
DNA is usually known as a biological carrier of information. However, scientists can use DNA as a building material to make microscopic structures. These DNA structures can self-assemble through Watson-Crick base pairing, which makes DNA a versatile structural material. The thermodynamics of DNA hybridization also contributes a great deal to how DNA structures hybridize. In a solution containing two complementary DNA strands, the equilibrium behavior can be predicted quantitatively. This stems from the fact that we can model hybridization as a simple bimolecular reaction with an equilibrium constant derived from the sequences using the nearest neighbor (NN) model. However, in systems with multiple complementary strands, some of which compete with one another, the equilibrium behavior cannot be explained by this model.
For this research, we aim to observe, understand and predict the equilibrium behavior of these competitive mixtures directly from their sequences. Our specific scenario involves two strands, A and B, which are partially complementary to each other. Two other strands, D1 and D2, are displacement strands that compete with A and B. We find that our data does not agree with NN model predictions for reactions with one or two displacement strands. In the future, we would like to design new strands to further test the limits of this model.
Support: SMURF (Summer MRSEC Undergrad Research Fellowship)