Underwound DNA under Tension: Structure, Elasticity, and Sequence-Dependent Behaviors

DNA melting under torsion plays an important role in a wide variety of cellular processes. In the present Letter, we have investigated DNA melting at the single-molecule level using an angular optical trap. By directly measuring force, extension, torque, and angle of DNA, we determined the structural and elastic parameters of torsionally melted DNA. Our data reveal that under moderate forces, the melted DNA assumes a left-handed structure as opposed to an open bubble conformation and is highly torsionally compliant. We have also discovered that at low forces melted DNA properties are highly dependent on DNA sequence. These results provide a more comprehensive picture of the global DNA force-torque phase diagram.

Figure 1

Torque (a) and extension (b) traces for Sequence A, averaged over multiple single-molecule experiments. Dashed lines indicate phase boundaries for measurements at 24 pN.

Figure 2

Force dependence of elastic parameters of L-DNA. Measurements (black squares) are compared with theory discussed in the main text (red [light gray] lines). The extension data were also fit by the wormlike chain model (blue [dark gray] line).

Figure 3

Sequence dependence of melted DNA. Representative extension traces of single DNA molecules are shown for different DNA sequences. (a) Sequence dependence. Extension behavior is identical for all three sequences at 12 pN (upper traces) and differs at 3.5 pN (lower traces). (b) Reversibility illustrated using Sequence B. Extension behavior is reversible at high force, and shows hysteresis at low force.