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Ideas for Bachelor and Master's projects

Studying cell signalling using nanopatterning of receptor ligands on self-assembled DNA origami structures

In the context of the Danish National Research Foundation Centre of Excellence, CellPAT, we run a number of projects that use specifically designed DNA and RNA origami structures to position ligands in a predefined nanoscale pattern, allowing us to study how pattern recognition and avidity contribute to cell signalling and activation. The current projects are focused on the immune system and skin stem cells but we plan to expand to other biological systems in the future. A student project could typically be to design a 2D nano-pattern of sugar or peptide, characterize its structure using various biophysical methods (e.g. super-resolution and transmission electron microscopy) and analyze its functional interplay with cultured cells (signaling, uptake and toxicity).

Contact person: Professor Jørgen Kjems 

Selection and characterization of aptamers for complex biological mixtures

Aptamers are oligonucleotides that fold into specific 3D structures that allow them to exert numerous functions, including specific binding to various biomolecules such as proteins, lipids or metabolites. We select aptamers to viruses and cellular receptors as well as makinglarge-scale screens for aptamer sequence that can characterise complex biological samples (e.g. body fluids) and combine this with multiomics analysis and mass spectrometry to identify new biomarkers. A student project could typically be to select an aptamer for a specific viral or cellular protein and test its biological function in test tube and cell culture assays.

Contact person: Professor Jørgen Kjems 

Biosynthesis and function of circular RNA

CircRNAs are covalently joined RNA molecules that show tissue- and age-dependent expression in metazoans. We combine high-throughput sequencing, biochemical analysis and cell biology to understand how circRNAs are formed, how they regulate gene expression and how they function in development. We also design circRNA vectors for therapeutic applications. A student project could typically be design and synthesis a circRNA for more durable protein expression and test it cell culture and animal models.

Contact person: Professor Jørgen Kjems