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A detailed description of the conformational plasticity of double strandedDNA (ds) is a necessary framework for understanding protein-DNA interactions.Until now, however structure and kinetics of the transition from the basicconformation of ds-DNA (B state) to the 1.7 times longer and partially unwoundconformation (S state) have not been defined. The force-extension relation ofthe ds-DNA of lambda-phage is measured here with unprecedented resolution usinga dual laser optical tweezers that can impose millisecond force steps of 0.5-2pN (25 C). This approach reveals the kinetics of the transition betweenintermediate states of ds-DNA and uncovers the load-dependence of the rateconstant of the unitary reaction step. DNA overstretching transition resultsessentially a two-state reaction composed of 5.85 nm steps, indicatingcooperativity of ~25 base pairs. This mechanism increases the free energy forthe unitary reaction to ~94 kBT, accounting for the stability of the basicconformation of DNA, and explains the absence of hysteresis in theforce-extension relation at equilibrium. The novel description of the kineticsand energetics of the B-S transition of ds-DNA improves our understanding thebiological role of the S state in the interplay between mechanics andenzymology of the DNA-protein machinery.

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