Kinetics of double stranded DNA overstretching revealed by 0.5-2 pN force steps

Abstract

A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation of ds-DNA (B state) to the 1.7 times longer and partially unwound conformation (S state) have not been defined. The force-extension relation of the ds-DNA of lambda-phage is measured here with unprecedented resolution using a dual laser optical tweezers that can impose millisecond force steps of 0.5-2 pN (25 C). This approach reveals the kinetics of the transition between intermediate states of ds-DNA and uncovers the load-dependence of the rate constant of the unitary reaction step. DNA overstretching transition results essentially a two-state reaction composed of 5.85 nm steps, indicating cooperativity of ~25 base pairs. This mechanism increases the free energy for the unitary reaction to ~94 kBT, accounting for the stability of the basic conformation of DNA, and explains the absence of hysteresis in the force-extension relation at equilibrium. The novel description of the kinetics and energetics of the B-S transition of ds-DNA improves our understanding the biological role of the S state in the interplay between mechanics and enzymology of the DNA-protein machinery.