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BP: Fachverband Biologische Physik
BP 18: Focus session: Integrative Structural Modeling
BP 18.2: Vortrag
Mittwoch, 11. März 2026, 11:00–11:15, BAR/0106
Extending the Fluorophore Dye Library for FRET-guided Modeling — •Isolde Kirk1, Felix Erichson1, Josephine Meitzner1, Patrick K. Quoika2, and Richard Börner1 — 1Laserinstitut Hochschule Mittweida, Mittweida, Germany — 2Technische Universität München, Munich, Germany
Integrative structural modeling combines experimental observables with computational methods to obtain realistic descriptions of biomolecular structures and their dynamics. One such approach integrates Förster Resonance Energy Transfer (FRET) and dynamic fluorescence anisotropy with molecular dynamics (MD) simulations. Ensuring comparability between experiment and simulation requires realistic modeling of fluorescent dyes in silico. In practice, existing dye libraries do not cover the full range of available fluorophores, including phosphate-backbone-linked carbocyanine (Cy) dyes. We therefore modeled and parametrized a FRET dye pair of Cy3 and 5 with a backbone-linked Cy3 fragment for MD simulations. We used Gaussian to assign partial charges with the restrained electrostatic potential method, as implemented in Antechamber, yielding several parametrization variants. The dye fragments were then incorporated into a DNA hairpin model and characterized using MD simulations with GROMACS. Depending on the parametrization, the DNA hairpin showed different structural responses, ranging from stable dye intercalation to partial helix destabilization. One parametrization showed agreement with the experimental data and therefore provides a validated extension for future FRET-guided modeling.
Keywords: DNA; FRET; MD simulation; dye modeling; integrative modeling