Universität Bonn

Biophysical Chemistry - Prof. Dr. U. Kubitscheck

Biophysical Chemistry
Prof. Dr. U. Kubitscheck
Ulrich Kubitscheck jpg
© U. Kubitscheck

Biophysical Chemistry

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Our work group is devoted to the analysis of molecular dynamics in the context of biological or biomimetical systems; our core area is the analysis of molecular kinetics within supra-molecular complexes on the single molecule level.

We employ state-of-the-art light microscopy techniques like confocal scanning microscopy and single-molecule microscopy using different illumnation techniques.

Our labs are equipped for the preparatory biochemistry and all standard protocols from cell to molecular biology.

A further key aspect of our work is the development of new or the improvement of existing light microscopic methods; current emphases are light sheet fluorescence microscopy (LSFM), confocal LSFM and 3D particle tracking.

Our research areas are:
(i)Analysis of molecular structure and dynamics in biological systems and of kinetic processes in supramolecular complexes
(ii)Development of high performance light microscopy techniques

Research Topics

Analysis of the Transport and Nuclear Export of RNA Particles in vivo

RNA transport 2
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Single Export Event
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Simplified Principle of the mRNA Export

Complexes of mRNA molecules, proteins and export factors during the export through a nuclear pore complex in the nuclear envelope. The DEAD-box RNA helicase Dbp5 is located at the cytoplasmic face of the pore. The removal of the export factors by Dbp5 accomplishes the directionality of the mRNA export.

Light Sheet Fluorescence Microscopy (LSFM)

Building a microscope 2
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Beam path of the first generation of our custom-developed light sheet fluorescence microscope (from 2012).

Development of a Dedicated Light Sheet Microscope for Expanded Samples


Simultaneous and fast image acquisition in two colors

For large and transparent samples up to a volume of 20x20x2 mm³

Automated, stable image acquisition for hours

Building a microscope 3
© Uni Bonn
© Uni Bonn

Design of New Light Sheet Profiles

Improvement of the Optical Resolution and Imaging Frame Rate

(1) Limited resolution and field size when using a light sheet with a Gaussian intensity profile

(2) Reduction of the light sheet thickness by using Bessel beam illumination

(3) Fast frame rates using thin light sheets by horizontally dithering a „lattice“ of Bessel beams

Expansion Microscopy

Physical expansion of samples allows to resolve finest details.
An effective super resolution microscopy becomes possible using conventional techniques.

Transparent specimen
Refractive index identical with that of water

Fixed samples only

ExM 2
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ExM 3
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Light Sheet Expansion Microscopy of Mouse Brain Sections

(A) Mouse dentate gyrus granule cells expressing EGFP. Maximum intensity projection of an expanded mouse brain slice, imaged with a custom LSFM.
Size 1150 x 1010 x 483 µm³ (40 z-stacks, step size of 300 nm, 15% overlap), (B) Magnification of the ROI marked in A, lateral field size 236 x 244 µm2, (C) 3D view of B comprising 864 slices of the stack. In red the segmentation and tracing of one neurite, (D) dendrite with its dendritic spines segmented and reconstructed in 3D (see ROI marked in B).

Analysis of the mode of action of antibiotics on bacteria

Goals and Approaches

Visualize components of the cell wall biosynthesis machinery (CWBM) in Staphylococcus aureus
•Generation of strains expressing labeled CWBM components
•Super resolution microscopy
•Visualization of protein and membrane microdomains

Study the impact of antibiotics on localization
•Antibiotics with varying degrees of membrane impairment
•Time-resolved super resolution microscopy
•Monitor cell viability

Quantify dynamics between CWBM components and antibiotics in vitro
•Membrane bilayer systems
•Study the impact of membrane properties

Bacterien Antibiotika
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S. aureus 1
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Concept ad Central Question:

How do antibiotics affect the organization of the cell wall biosynthesis machinery (CWBM)?

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