Loop dependence of the dynamics of DNA hairpins

The kinetics of unwinding of DNA hairpins with varying loop sizes L was mon itored using time-resolved absorbance measurements after a laser temperatur e 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 po ly(dA) strands, in close agreement with the scaling of loop-closure probabi lity expected for semiflexible polymers. In contrast, equilibrium measureme nts show that the hairpins with smaller loops are stabilized by a factor th at 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, to gether 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 dep endence of the relaxation times, obtained primarily at temperatures below t he melting temperature from fluctuation correlation spectroscopy measuremen ts 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.; Lib chaber, A. Phys. Rev. Lett. 2000, 85, 2400). A configurational diffusion mo del to describe hairpin dynamics is presented in which transient trapping i n misfolded loops is sufficient to explain the change in the sign of the ac tivation energy in the two sets of measurements.