Recent Single-Molecule Studies of DNA Structure and Stability
ABSTRACT
I will present two recent experimental studies from our lab, each using single-molecule techniques to reveal interesting, overlooked features of DNA.
In the first study, we examine the poloidal orientation of DNA minicircles. Because DNA bending energetics depend on sequence, a minicircle is expected to adopt a preferred inside-out orientation. Using atomic force microscopy, we directly visualize this orientation by tracking a protein marker placed at defined positions along the minicircle. Coarse-grained simulations reproduce the experimental results and suggest future possibilities for creating unusual DNA gadgets.
In the second study, we examine how single-stranded overhangs influence the stability of short DNA duplexes. Using single-molecule FRET, we find that changing a single nucleotide at the distal end of an overhang can dramatically alter duplex dissociation kinetics. Molecular dynamics simulations suggest that the overhang folds back and stacks against the duplex, acting as a molecular antenna that modulates strand separation.
Together, these studies show that sequence exerts surprisingly strong control over DNA mechanics and stability at short length scales.
