Bubbles, Free Ends and the Kinetics of Force-Induced DNA Melting

Abstract

Application of a stretching force to the opposite ends of torsionally unconstrained double stranded (ds) DNA leads to its abrupt 1.7-fold elongation at a force of roughly 65 pN. While the disruption of base stacking is understood to drive the length change, the extent to which base pairing remains intact continues to be controversial. Here we present kinetic data on the overstretching transition including new results on the pulling rate dependence of the DNA overstretching transition at different solution ionic strengths. It is now clear that the observed DNA overstretching transition indeed occurs in two very different modes, though bases are unpaired in both. In the first mode, DNA peels sequentially from any free end. In the second mode, bubbles of several hundred cooperatively melted base pairs appear along heterogeneous DNA. Kinetic data further reveals that the transition state is much closer to dsDNA than to the melted form. Our results also show that only the rate of base pair closing is strongly affected by force, which destabilizes each base pair not by facilitating melting but by inhibiting closing. Finally, we discuss how the switch between the peeling and internal FIM modes is affected by solution ionic strength, temperature, DNA sequence heterogeneity and the DNA pulling rate.