Stanford

“Using Polymer Physics Theory to Understand the Structural TransiDon from Right-Handed to LeI-Handed DNA”

ABSTRACT

By significantly undertwisDng a DNA molecule under constant applied tension, single-molecule magneDc tweezer experiments can induce a structural transiDon from canonical right-handed B- DNA to leI-handed L-DNA. When the molecule is held at low tension, its response to minimal underwinding and overwinding is symmetric. The molecule coils into a plectoneme and its extension decreases dramaDcally. However, as tension increases, the molecule remains extended in response to undertwisDng, signaling the transiDon from B- to L-DNA. We study the B-L transiDon by developing a theoreDcal model of DNA that accounts for its elasDc energy, applied force and torque, and the energeDcs of base pair transiDons. Results from our model recapitulate experimental data from extension experiments as well as data from torque-measurement experiments. Our theory predicts a novel cooperaDve factor that is both force- and torque-dependent. This factor promotes segregaDon of B- and L-DNA base pairs and is most prominent at lower tensions. In future work, this model may serve as a foundaDon for understanding the B-L transiDon in more complex cellular environments.