B5.1: “Caged fluorophores for single-molecule super-resolution microscopy and light-induced recepetor clustering"

This PhD student will investigate the photoactivation properties of caged fluorophores synthesized in PhD thesis A2.3, such as photoactivation kinetics, photostability and brightness. These studies will be performed at the single molecule level on (i) isolated fluorophores as well as (ii) attached to a biological model structure (tubulin filaments, fluorescence labeling via immunofluorescence). This PhD student will then investigate other caged fluorophores synthesized in PhD thesis A2.3 and aim for a set of spectrally-distinct fluorophores caged by the same chemical group to facilitate multi-color SMSRM (by using one wavelength for uncaging (e.g. 405 nm) and various wavelengths to read out the fluorescence signal of the synthetic dyes). In addition, the PhD student will work together with PhD theses B4.1 and B4.2 and characterize photoactivatable tris-NTA dyes (PA-trisNTA) at the single-molecule level.


B5.2: “Complex RNA folding pathways studied with single-molecule FRET and caged intermediates”

This PhD student will employ single-molecule FRET to study the folding pathways of RNA molecules. The student will work in close collaboration with PhD thesis B1.2 (synthesis of complex RNA and site-specific labeling with synthetic fluorophores was recently established) and PhD thesis A2.1 (caged oligonucleotides). The focus of this PhD thesis will be to analyze complex folding pathways as they are typically found in large RNA molecules with enzymatic activity; the set of kinetic rates of multiple (follow-up) folding and rearrangement reactions are typically inaccessible by conventional single-molecule FRET experiments.