Studying the thermal fluctuations of DNA molecules reveals not only a wealth of interesting equilibrium and non-equilibrium statistical mechanics, but is also of importance for understanding the dynamics of DNA in vivo. An instance of the latter is in the context of regulatory functions that require collaborative interactions of distant operator sites on the DNA molecule.; These thermal fluctuations are extremely sensitive to mechanical constraints, such as super-coiling or mechanical tension in the DNA. The natural force scale fc on which these fluctuations are sensitive to tension is related to the molecule's persistence length lp by fc = kBT/lp = 80 fN.; We studied the dynamics of single DNA molecules subjected to tension under equilibrium and non-equilibrium conditions using a modified scanning-line laser trap. The studies of the hydrodynamic and entropic forces associated with DNA molecules in solution required the ability to study and manipulate single DNA molecules with unprecedented accuracy. Towards this end, we developed and calibrated an all-optical, scanning-line tweezer based apparatus, which allows us to generate constant forces between 20 fN and 3pN. We also developed a fast, high-resolution (50nm) particle position measurement scheme that is based on synchronous detection of forward-scattered laser light during a line scan of the beam. Using these techniques, we studied the behavior of lambda-DNA molecules that were relaxing to an equilibrium configuration as well as those already at equilibrium. In the non-equilibrium studies we found good general agreement with the predictions derived from the wormlike-chain (WLC) model for extended DNA molecules. Studying the energies involved in these experiments also revealed that the hydrodynamic drag of the DNA molecule contributes almost a third of the energy dissipated due to the viscous forces in the system. In the equilibrium studies we observed a decrease of the fundamental time constant with increasing extension of the molecule. This suggests that the change in spring constant dominates changes in the intra-chain hydrodynamic coupling between segments as the Gaussian coil unravels into an extended conformation.
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