Random walk of pVIc peptide on confined, two-dimensional DNA-origami carpets

Freyer, P. (2013) Random walk of pVIc peptide on confined, two-dimensional DNA-origami carpets. Bachelor's Thesis, Physics.

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Abstract

This thesis is a follow-up of single-molecule studies that have characterized one dimensional random walk of the 11 amino-acid peptide pVIc along DNA. It was originally aimed at obtaining further insight to pVIc sliding on two dimensional DNA-origami sheets with characteristic size of 50nm x 150nm. Making use of TIRF microscopy and custom analysis software, particle trajectories could theoretically be obtained at accuracies around 20 nm. This accuracy could however not be utilized due to large (80nm) spatial oscillations of the field of view (FOV), that remain unexplained. In addition, from the one-dimensional diffusion constant of pVIc a predicted camera exposure times of maximum 20us would be necessary to make appropriate MSD graphs and determine the two-dimensional diffusion coefficient. As this was not possible (camera exposure time minimum of 2,4ms for stream acquisition (movies)), we tried to extract quantitative information from the Gaussian fits of the fluorescent spots. I will present these results including the typical trajectories that pVIc shows at 16ms exposure time, with the mentioned FOV oscillations. I hope to give a good picture of the ups and downs of analysing a large number of molecules simultaneously and the obstacles that need to be overcome in order to obtain more meaningful results.

Item Type:	Thesis (Bachelor's Thesis)
Degree programme:	Physics
Thesis type:	Bachelor's Thesis
Language:	English
Date Deposited:	15 Feb 2018 07:54
Last Modified:	15 Feb 2018 07:54
URI:	https://fse.studenttheses.ub.rug.nl/id/eprint/11305

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