Atomic Force Microscopy of dynamic protein DNA interactions

In this thesis a dedicated Atomic Force Microscopy (AFM) setup is used for imaging biochemical reactions with molecular resolution. The basis for the high resolution of AFM is the combination of a small probe, close proximity to the sample and a short-range interaction between the probe and the sample. The tip-sample interaction forces that are used in AFM allow imaging in various environments, including physiological buffers. However, although a decade has passed since DNA was first imaged using an AFM, most studies are still performed in air, and by doing so the sample is dehydrated and fixed. Visualization of protein-DNA interactions in physiological buffer would exploit the advantages of AFM that make it a unique tool for studying these reactions, namely its molecular resolution of functional complexes in combination with only limited sample preparation. It is shown in this thesis that high-resolution topography maps of these biomolecules can be measured with AFM reproducibly, over a long period of time, and with a fairly good temporal resolution. A careful optimization of the imaging parameters is required for this