Page - 57 - in Charge Transport in DNA - Insights from Simulations

4.3 IrreversibilityofDNAStretching inSimulations Figure4.8: Distance/force profile in the stretching/relaxing simulations of A13. Black – stretching (increasing force), colored – subsequent relaxation from the pointsA,B,C andD; left – external force removed abruptly, right – force decreased to zero gradually. Table4.3: Final structures after the stretching/relaxing simulations. force removedabruptly forcedecreasedgradually fromA fromB fromC fromD fromA fromB fromC fromD A5 helix helix helix ladder A5 ladder ladder ladder ladder A9 helix helix ladder helix A9 helix ladder ladder separation A13 helix helix helix helix A13 helix ladder ladder ladder G5 helix helix ladder ladder G5 ladder ladder ladder separation G9 helix helix helix ladder G9 ladder ladder ladder separation G13 helix helix helix helix G13 ladder ladder ladder separation was not always the casewhen the forcewas removed already in the ladder state of theDNAoligomer. In some simulations, the ladderwas preserved even in the free simulation whereas the other simulated DNA species returned to a helical conformation. The situation changes dramatically when passing to the simulation with a grad- ual decrease of the force. Already when the external force was being switched off from themidpoint of the helix–ladder transition (B), the helical conformation does not recoverwithin the simulation time. This hysteresis emphasizes the irre- versible character ofDNAstretching in the performed simulations. Its evenmore distinctdemonstration is theseparationofDNAstrandsobserved in fourof thesix simulations after the reversal of external force inpointD. 57