Infoscience

Thesis

Research in the field of single biopolymers using scanning probe microscopy

Current thesis is devoted to the investigation of biopolymers using AFM, a well established and widely used technique. To begin with, we studied processing of AFM images and its automation. Our software product, DNA Trace, permit one to quickly extract scientifically meaningful data from a huge number of AFM scans. Then, this program enabled us to perform a study on how polymers, with DNA as a model, change their conformation from three to two dimensions upon their deposition onto the surface. DNA molecules suit well for such an investigation as they are studied in detail, easy to deposit onto mica surface, have relatively large persistence length to be traced on the images and, the most important, relax from 3D to 2D, the timescale of this process being in order of tens seconds to minutes. Besides, we introduced so-called concentration function to describe numerically such transition and adapted formulas of the theory of diffusion to polymers. We depicted this process as a diffusional propagation of relaxation of short segments of polymer. The results we have obtained are very promising and hopefully will lead to the better understanding of the theory of polymers, as the latter are widely used in all areas of industry. Then, this work describes the possibility to increase the sensitivity of cantilever deflection detection. We etched a diffraction grating on the backside of cantilever and used diffractive rather than mirror reflection of a laser beam, which gave geometrical advantage. We also used position-sensitive duo-lateral diode in this setup and finally got the increase of sensitivity of about 5 - 10 times compared to common detection scheme. Finally, a big chapter of this thesis is devoted to force spectroscopy, the technique, which permit one to measure forces of interaction between biomolecules and thus obtain kinetic parameters of interaction. We studied barnase - barstar pair and then flaviviral proteins - putative cell receptors interaction. The results obtaining by the latter study will hopefully lead to the model of flaviviral - cell membrane fusion.

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