Persönlicher Status und Werkzeuge

Welcome to the Simmel lab - Systems Biophysics and Bionanotechnology

Vision

Our goal is the realization of self-organizing molecular systems that are able to respond to their environment, compute, move, take action. On the long term, we envision autonomous systems that are reconfigurable, that can evolve, develop, or even learn.

Current Research Highlights

Dynamical diversity of a compartmentalized biochemical oscillator: In this collaborative study performed with the groups of Erik Winfree (Caltech) and Elisa Franco (UC Riverside), we encapsulated a programmable biochemical feedback oscillator based on transcription reactions into microemulsion droplets with sizes in the range of 16 fL to 33 pL. We evaluated thousands of oscillator reactions from individual droplets and found large variability in the period and amplitude of the oscillations. The variations are much larger than expected from a simple Poisson-partitioning model and can be traced back to broader-than-Poisson variability in enzyme activity in the droplets.

M. Weitz, J. Kim, K. Kapsner, E. Winfree, E. Franco, F. C. Simmel, Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator, Nature Chemistry 6, 295-302 (2014). http://dx.doi.org/10.1038/nchem.1869 


Single molecule studies on lithographically arranged DNA origami platforms: By combining DNA self-assembly and electron-beam lithography on transparent glass substrates, we created a DNA origami microarray, which is compatible with the requirements of single molecule fluorescence and super-resolution microscopy. We utilized the microarray to characterize the performance of DNA strand displacement reactions localized on the DNA origami structures. We find considerable variability within the array, which results both from structural variations and stochastic reaction dynamics prevalent at the single molecule level.

M. Scheible, G. Pardatscher, A. Kuzyk, F. C. Simmel, Single Molecule Characterization of DNA Binding and Strand Displacement Reactions on Lithographic DNA Origami Microarrays, Nano Letters 14, 1627-1633 (2014). DOI: 10.1021/nl500092j


Communication and computation of bacteria in microemulsion droplets: We describe the encapsulation of bacteria within spatially extended arrays of water-in-oil microemulsion droplets. We find that chemical signals – genetic inducers – diffuse from droplet to droplet, and thus influence gene expression in the bacteria. As shown in the figure on the left, also computational receiver bacteria were engineered that integrate two chemical signals with a genetic AND-gate, and respond by GFP expression only in the neighborhood of two distinct types of reservoir droplets.

M. Weitz, A. Mückl, K. Kapsner, R. Berg, A. Meyer, F. C. Simmel, Communication and computation by bacteria compartmentalized within microemulsion droplets, Journal of the American Chemical Society 136, 72-75 (2014). dx.doi.org/10.1021/ja411132w


Synthetic DNA-based lipid membrane channels: In collaboration with the Dietz group at TUM and Michael Mayer at U Michigan, we created an artificial ion channel based on a DNA nanostructure. The DNA channel consists of a membrane-spanning DNA six-helix bundle and a “cap” structure formed by 54 parallel DNA double helices. The cap structure adheres to one side of a lipid bilayer membrane via 26 cholesterol “anchors”, while the central stem pierces through the membrane. The hollow core of the stem forms an ion conductive 2 nm wide channel through the membrane. Folding and membrane insertion of the structures as well as their electrical properties were investigated using electron microscopy, electrophysiological measurements, and single-molecule translocation experiments.

M. Langecker, V. Arnaut, T. G. Martin, J. List, S. Renner, M. Mayer, H. Dietz, F. C. Simmel, Synthetic lipid membrane channels formed by designed DNA nanostructures, Science 338, 932-936 (2012).