Competition between DNA Secondary Structures

Paper:

• • • Cynthia Shaheen, Bianca Caminada, Alexis Hilts, Ruby Wei, Jay Botham, Rebecca Johnson, Nane Vardanyan, Eric Boateng, Sabrina Leslie, "Stemless molecular beacon probes for single-molecule detection of supercoil-induced DNA denaturation," submitted to npj Biological Physics and Mechanics (2025).

Supercoiled DNA exists in all cells, however the impact of DNA supercoiling on local structure, and thus on gene regulation, is not fully understood. Statistical mechanics theory predicts changes to local DNA structure driven by the torsional strain created through supercoiling. These structural changes can have important implications in gene regulation.

In this project, we designed plasmids (circular DNA) with controlled structures. We predicted the structural transitions of DNA under various biological conditions through simulations based on the competition of energy, and we compared it against experimental results.