Insights into DNA intercalation using combined optical tweezers and fluorescence microscopy

The functioning of a single cell, and indirectly that of complete organism, is due to a large number of interlocking biological processes. These processes essentially comprise of a large number of highly specific interactions between different individual biomolecules, such as nucleic acids, proteins, lipids and other small organic molecules. One of the most important interactions within the cell is the interaction of protein molecules with deoxyribonucleic acid (DNA). DNA contains the genetic information of an organism and by duplicating itself very accurately before cell division, it is responsible for the transfer of this information from one cell to the next. Another central role of the DNA in the living cell is its involvement in the process of transcription and translation, which are the essential steps towards the synthesis of proteins. Many technologies have been developed that are able to measure biomolecular interactions, but they are limited to measurements on large number of interactions (ensemble measurements). During the past 20 years we have witnessed the development of different single molecule techniques such as magnetic tweezers, atomic force microscopy, fluorescence microscopy and optical tweezers, that allow the measurement of one molecule at a time, or the interactions between a small number of molecules. This ‘single molecule’ approach provides detailed information about the interactions that cannot be retrieved using bulk techniques, because the effects would be averaged and therefore not observable. In this thesis we set out to develop an instrument which is capable of probing the change in the mechanical properties of a single double-stranded DNA molecule as it is interacting with protein molecules, having the capability to detect the number and location of the protein molecules on the DNA simultaneously. This allows us to directly correlate the effect of protein binding on the mechanical properties of the DNA on a single molecule level.