Master’s Projects Available: “Short Range Interactions of Fluorescent Dyes”

We are currently offering a masters research project for students of Experimental Physics, or for preference, Nanomaterials Science in our lab (Molecular Biophysics). The research concerns energy transfer and quenching effects observed in fiducial markers for CLEM* and fluorescent labels used in super-resolution microscopy. You will find the full project description and contact details after the break.

Short Range Interactions of Fluorescent Dyes

Fluorescence Labeling is a versatile tool in (Life)Science which permits functional imaging of biological (cells, tissue) as well as non-biological samples (catalytic particles, geological samples ..) alike. While the photophysical parameters of fluorescent labels are generally well established in bulk, and generally change only little when attached to a molecule of interest, the interactions of fluorophores with their environment and each other are nevertheless of great interest. This is especially the case with the more routine usage of super-resolution microscopy techniques, that require an ever increasing labeling density for optimal performance.

In this project, the student will characterize the photophysical parameters (spectrum, intensity, fluorescenct life time, possibly anisotropy) of dyes in close contact with other dyes or quenchers in the sub-Förster-distance regime. For this, he will utilize molecular rulers in the form of single- and double stranded DNA. While the DNA with well defined internal (base-modified) attachment points will be purchased, we will have to perform the attachment of a/multiple dye(s) in our wetlab; this requires the refinement of attachment protocols to produce stoichometrically pure samples.

As all interactions are both distance and orientation dependent, the student will also expand a model developed in the lab that will allow to compare experimental data to theoretical predictions.

By the end of this project, the student will have a deeper understanding of the photophysics of fluorescence dyes, in particular their interaction via dipole-dipole energy transfer (Förster) or tunneling (Dexter). They will have learned how to design and refine DNA-based molecular rulers that allow the measurement of the effects, as well have been introduced to the optical techniques needed to measure them both in bulk as well as the single fluorophore level.

contact: Gerhard Blab (

* CLEM — correlative Light and Electron Microscopy


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