Kinetics of DNA force-induced melting

Abstract

Once stretched beyond its B-form contour length, double-stranded DNA reveals a sudden increase in length over approximately constant force at about 65 pN. During this conformational transition, DNA base pairing and base stacking are disrupted, converting double stranded DNA (dsDNA) into single stranded DNA (ssDNA). While thermodynamic and recent chemical labeling and fluorescence imaging experiments indicate that this transition is analogous to thermal melting, the kinetics of DNA force-induced melting have not been characterized. We present a predictive model of force-induced melting in which thermal fluctuations induce local melting and re-annealing of DNA. These fluctuations are stabilized by the application of tension during the overstretching transition, favoring the conversion to ssDNA as the applied force is increased. This model quantitatively predicts small changes in the melting force as the pulling rate is varied. We verify that the DNA melting force varies with pulling rate, consistent with this model, and that DNA force-induced melting depends only weakly on pulling rate at slow pulling rates, as melting occurs cooperatively with a domain size of 100-200 base pairs. As the pulling rate is increased beyond the natural duplex opening rate, the melting force depends strongly on pulling rate and the melted domain size decreases to 5-10 base pairs, as the DNA is ripped sequentially from the free ends (or any boundary). The final strand separation occurs at much higher forces, representing the nonequilibrium ripping of the most stable regions that remain at the end of the low force transition. The results indicate that force only weakly enhances base pair opening, while strongly inhibiting base pair closing.