Loop dependence of the dynamics of DNA hairpins

The kinetics of unwinding of DNA hairpins with varying loop sizes L was monitored using time-resolved absorbance measurements after a laser temperature jump. The characteristic time for forming hairpins is found to scale with the loop size as L2.0 +/-0.2, for loops consisting of both poly(dT) and poly(dA) strands, in close agreement with the scaling of loop-closure probability expected for semiflexible polymers. In contrast, equilibrium measurements show that the hairpins with smaller loops are stabilized by a factor that is much lar-er than can be accounted for simply by the entropic cost of bringing two ends of the polymer to-ether. This excess stability of smaller loops partitions into the opening times, which are found to decrease as L-2.0 +/-0.3. The temperature dependence of the observed relaxation times, together with the equilibrium measurements, yields negative activation energy (approximate to -11 +/- 2.3 kcal/mol) for the closing step at temperatures near the melting temperature of the hairpins. In contrast, temperature dependence of the relaxation times, obtained primarily at temperatures below the melting temperature from fluctuation correlation spectroscopy measurements on similar hairpins, yield activation energies for the closing step that are positive (Bonnet, G.; Krichevsky, O.; Libchaber, A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 8602; Goddard, N. L.; Bonnet, G.; Krichevsky, O.; Libchaber, A. Phys. Rev. Lett. 2000, 85, 2400). A configurational diffusion model to describe hairpin dynamics is presented in which transient trapping in misfolded loops is sufficient to explain the change in the sign of the activation energy in the two sets of measurements.