6. Unzipping of DNA at controlled force

When in doubt, use brute force.

Ken Thompson (1943)

A significant group of techniques in biophysics are capable of applying forces to individual molecules. Some of them directly control the force such as the magnetic tweezers. Some others apply forces by means of indirect control parameters such as the optical tweezers. Apparently, there should be no difference between both kinds of techniques. However, the control parameter determines what magnitude is fixed (force or extension) and what magnitude fluctuates (extension or force, respectively), while establishing the type of experiments that can be performed. Recent theoretical studies have shown the inequivalence between statistical ensembles for the elasticity of polymers [123]. The question that emerges here is whether this inequivalence can be observed experimentally.

Detailed studies of DNA unzipping at Controlled Force (CF) have been carried out with magnetic tweezers [23]. The results show how unzipping is always a non-equilibrium process with dissipation of energy that leads to large hysteresis cycles [147]. These experiments have been accompanied with theoretical studies of the process that shed light into the phenomenon [29]. On the other side, the unzipping experiments at Controlled Position (CP) [24,148,25] have been capable of obtaining more information from the internal structure of the DNA molecule. So, the published works on DNA unzipping use different experimental techniques, different molecular constructs and different instruments. How the unzipping processes compare when the only difference is in the choice of the control parameter?

This chapter describes how optical tweezers combined with a high bandwidth force feedback are capable of measuring the FDCs of the same molecular construct at CP and CF. The experimental data measured at CF can be analyzed with the tools developed up to now. In the end, we are able to directly compare the differences between one type of experiments and the other and determine the origin of the inequivalence of ensembles.

The work presented in this chapter is exploratory and descriptive and the obtained results have to be considered preliminary. Nevertheless, they raise interesting questions about DNA unzipping, disordered systems and non-equilibrium thermodynamics. The open questions exposed here will be answered in the future with more experiments and calculations.

JM Huguet 2014-02-12