TY - THES ID - 137132231 TI - In silico single-molecule Förster resonance energy transfer: Molecular dynamics simulations of fluorescently labelled DNA AU - Mertens, Steven AU - Harvey, Jeremy AU - Hendrix, Jelle AU - KU Leuven. Faculteit Wetenschappen. Opleiding Master in de chemie (uitdovend programma vanaf 2018-2019) (Leuven) PY - 2019 PB - Leuven KU Leuven. Faculteit Wetenschappen DB - UniCat UR - https://www.unicat.be/uniCat?func=search&query=sysid:137132231 AB - Fluorescence a phenomenon where certain chemical compounds emit light. A special variant of fluorescence, Föster resonance energy transfer (FRET), can be used to measure the distance between two points on a biomolecule. The shape of molecules can be determined by comparing predicted FRET values to experimentally measured FRET values. The predicted FRET values are based on prior research. The predictions are performed using a computational method known as accessible volume calculations (AV). Due to the simplified nature of AV calculations, the extend to which AV can be used to model experimentally observed values has been brought into question. The research in this thesis compared FRET values measured in experiments to those found via AV calculations. Ultimately, the goal was to find out whether AV calculations can successfully reproduce experimentally observed values. The comparison showed that, while the results of the AV calculations approached those found in experimental measurements, differences between the two remained. The research described in this thesis used a second computational method, molecular dynamics (MD), to investigate the cause of the differences between AV and experimental measurements. The conclusion was made that the differences are due to AV calculations overestimating the flexibility of certain parts of the molecule. Furthermore, AV calculations take into consideration improbable forms of the molecule. These forms are so improbable that they are practically impossible and not observed in experiments. ER -