This PhD thesis is about the statistical and thermodynamic properties of DNA unzipping studied with optical tweezers.
Chapter 2 contains a thorough description of the optical trapping principle and the Minitweezers instrument used in the experiments reported in this thesis. The physics laying behind the optical tweezers is explained step by step. The technical details about the implementation of the instrument are also given. The maintenance (calibration, design of new protocols) of the instrument completes the chapter. All the information is complemented in the appendices.
Chapter 3 focuses on the molecule of DNA. There is an introductory description of the structure of the DNA. This description sets the basis to understand the goal of the unzipping experiments performed with optical tweezers. Then the chapter describes the unzipping experiments and the models used to illustrate the phenomena observed.
Chapter 4 is a closer look to the statistical properties of the metastable states observed during DNA unzipping. The molecule of DNA is viewed as a system that exhibits cooperative transitions between its intermediate states. A toy model is developed to simplify and understand this phenomenon. This model also allows us to predict the experimental conditions under which sequencing of DNA by mechanical unzipping will be feasible.
Chapter 5 explains in detail how to extract the free energy of formation of duplexes of DNA from unzipping experiments. This is an original new approach in which the free energies of the building blocks of DNA (i.e., the base-pairs) are directly obtained. The chapter describes the analysis of the experimental data and the theoretical model that is used to reach this goal. The chapter concludes with a discussion about the salt dependence of free energies, one of the main conclusions of this thesis.
Chapter 6 is an exploratory study of DNA unzipping at controlled force. The chapter compares the controlled force experiments with those performed at controlled position and discusses the origin of the differences between them. There is also a brief investigation of the causes of the large hysteresis and irreversibility observed at controlled force.
Finally, chapter 7 sketches some future works and perspectives open by this thesis and summarizes the main conclusions derived from this PhD thesis.
JM Huguet 2014-02-12