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Schlierf Group - DNA and RNA secondary structures

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DNA hairpin structures

We are interested in the kinetic and thermodynamic parameters of DNA annealing. In order to address conformational kinetics of DNA hairpins we use single-molecule FRET to monitor nanometer length changes with sub-millisecond time resolution. 

Team members on the project: Andreas, Georg

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The attC hairpin

The attC hairpin is a crucial secondary DNA structure aiding Integron mediated recombination. Integron mediated recombination is the primary mode of acquisition of antibiotic resistance genes in bacteria. Interestingly, in vivo predominantly one of the two DNA cruciform strands are recombined. We are interested in the structural and thermodynamical differences between the top and bottom strand of the attC site aadA7. We use optical tweezers to characterise structural features and thermodynamic parameters of different DNA hairpins. 

Team members in the project: Matthias, Ann, Svea

RNA thermometers

Monitoring and reacting to changes of the ambient temperature is essential for bacterial and eukaryotic survival. The induction of expression of heat shock and cold shock proteins by changes of temperature is a well-known example of thermo-regulation. In bacteria the expression of many of these proteins is regulated by thermo-responsive non-coding RNA sequences, referred to as RNA thermometers. These hairpin-shaped RNA thermometers are evolutionary optimized intracellular temperature sensors.  The stability of RNA thermometers has been studied with NMR and CD spectroscopy. However, kinetic information about the temperature dependent dynamics are missing to understand the biological function in greater detail. To address these questions we perform smFRET experiments at different temperatures.

Team members on the project: Andreas, Frederic