Single-molecule stretching

Cui and Bustamante [66], Bennink et al. [43], Brower-Toland et al. [42], and Leuba and Zlatanova (unpublished results) have reported single molecule stretching... 

Molecules react because they move. They move internally—we have seen (Chapter 3) how the stretching and bending of bonds can be detected by infrared spectroscopy. Whole molecules move continuously in space, bumping into each other, into the walls of the vessel they are in, and into the solvent if they are in solution. When one bond in a single molecule stretches too much it may break and a chemical reaction occurs. When two molecules bump into each other, they may combine with the formation of a new bond, and a chemical reaction occurs. We are first going to think about collisions between molecules. 

Hummer and Szabo" demonstrated that in single molecule stretching experiments, the JE provides an expression for the work at different times, whereas from an experimental point of view it is of more interest to know the free energy difference between states at different extensions of the molecule. They show how this can be obtained and apply it in experiments. 

Thermodynamics of DNA interactions from single molecule-stretching experiments 02ACR159. 

Williams, M.C., Rouzina, L, Bloomfield, VA. 2002. Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res. 35 159-166. 

Here, we report on single-molecule stretching of native fibronectin and the influence of the compatible solutes ectoine and sarcosine on the mechanical properties, as revealed by the unfolding of the individual subunits and the overall persistence length of the macromolecule [131], In accordance with the preferential exclusion model, we found a significant stabilization of the protein structure in the presence of osmolytes but not an increase in unfolding forces. 

With the advent of nanotechnology, interest in the physics of small systems far from equilibrium has strongly increased. Suddenly, tiny systems in which thermal fluctuations prevail could be easily conceived and realized. Mechanically driven transformations, as carried out by single-molecule stretching experiments... 

Fig. 1 Force mode of AFM. (a) A schematic view of single molecule stretching, (b) Relation between piezo distance, D, cantilever deflection, d, and sample extension, E. The approach of the cantilever starts from position 1 on the tight to position 2 where the probe touches the sample surface. When the sample surface is rigid, the cantilever is pushed up to position 3 where the cantilever movement is reversed and the cantilever traces back to position 1 without hysteresis. When the sample surface is soft, cantilever deflection follows a curve from position 2 to 3 indenting the sample with the maximum depth of I. In the retraction regime, when a part of the sample is adhered to the probe, the cantilever shows a gradual or immediate downward deflection due to the tensile force from the sample. In this figure, the tensile material adhered to the probe is assumed to be a flexible polymer like material so that the downward deflection of the cantilever is inititdly small but rapidly increases to position 5 where the adhesion bond of the sample to the probe is broken abruptly (Reproduced from [66] with permission)...

Within the mixed quantum/classical approach, at each time step in a classical molecular dynamics simulation (that is, for each configuration of the bath coordinates), for each chromophore one needs the transition frequency and the transition dipole or polarizability, and if there are multiple chromophores, one needs the coupling frequencies between each pair. For water a number of different possible approaches have been used to obtain these quantities in this section we begin with brief discussions of each approach to determine transition frequencies. For definiteness we consider the case of a single OH stretch chromophore on an HOD molecule in liquid D2O. 

Figure 6. PuUing single molecules, (a) Stretching DNA (b) unzipping DNA (c) mechanical unfolding of RNA, and (d) mechanical unfolding of proteins. (See color insert.)...

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