4. Metastable intermediates in DNA unzipping


When individuals join in a
cooperative venture, the power
generated far exceeds what they
could have accomplished acting
individually.


Richard Buckminster Fuller (1895-1983)



From a pure physical point of view, the unzipping of DNA can be regarded as a process of fracture, in which the strength applied to the two strands produces the disruption of the base-pairs [124]. The FDC of unzipping has similar properties to the Barkhausen noise observed in the magnetization of ferromagnetic domains, paper tearing or earthquakes. The characteristic fingerprint in all of these cases is the sawtooth-like signal. The slopes of the sawtooth pattern correspond to the accumulation of energy (elasticity), while the drops in the signal are related to the release of energy (breakage). Bonnott and coworkers [125] have measured stress vs. strain curves on martensitic materials that look very similar to the FDC of DNA unzipping, showing that both phenomena exhibit the typical properties of fracture. Similarly, sawtooth-like FDCs have been observed in pulling experiments of gold nanowires with scanning tunneling microscopy [126]. In one of his articles about DNA unzipping with microneedles, Bockelmann et al. already identified the stick-slip motion (i.e., slopes and drops) of the unzipping fork, which is a characteristic signature of the cracking effects.

The unzipping of DNA can be studied globally, considering the succession of opening base-pairs as part of a whole process of fracture. The detailed information about the local effects is neglected and the relevant conclusions focus on the statistical properties of the intermediate states. In this approach, the DNA molecule is regarded as a disordered statistical system due to the randomness of the base-pair sequence. A theoretical work by Lubensky and Nelson [29] explored the statistical properties of DNA unzipping at constant force, based on the experimental results of their collaborators [23]. One of the main results of that paper was the calculation of the size of the opening fork as the mean unzipping force is approached.

This chapter focuses on the statistical properties of the metastable intermediate states observed in DNA unzipping experiments at controlled position. The study allows us to deepen into the intrinsic mechanism that induces the opening of base pairs. Besides, the analysis of the experimental data is accompanied with the development of a toy model that contains the essential ingredients needed to reproduce the unzipping process. It is useful to establish what are the experimental conditions that permit to break up the metastable states that are observed during the unzipping into single base-pair events. Eventually, this might be useful to set the basis for sequencing DNA by force, a potentially interesting application in the field of biotechnology. A limiting factor in unzipping is the accuracy at which individual base pairs along the DNA can be resolved. Indeed, the unzipping process, even if carried out reversibly (i.e., infinitely slowly), shows a progression of cooperative unzipping/rezipping transitions that involve groups of base pairs of different sizes. These Cooperatively Unzipping Regions (CURs) of base pairs breath in an all-or-none fashion hindering details about the individual base pairs participating in such transitions. Here it is shown a Bayesian technique useful to extract as much information as possible from the noisy experimental data.

The treatment of the experimental data that exhibits CURs is complemented with a toy model. This model captures the very essential ingredients that reproduce the unzipping FDCs and the properties of the CURs. The advantage of such model with respect to the mesoscopic model introduced in the previous chapter is that with the toy model it is easier and faster to extract statistical properties of CURs. Indeed, it is computationally less demanding and the simulations of unzipping experiments can be extended to thousands of different sequences. This gives valuable information about the dependence of the CURs on the experimental conditions (trap stiffness, base-pair energies, etc.).

To sum up, here we will treat the DNA unzipping of long molecules as a whole phenomenon.



Subsections
JM Huguet 2014-02-12