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).

Plasmonic nanoparticle helices constructed with DNA origami: In collaboration with the groups of Tim Liedl (LMU Munich) and Alexander Govorov (Ohio University), we arranged metallic nanoparticles into defined helical shapes along 24 helix bundles made with the DNA origami technique. Interactions of plasmon excitations along the helices lead to a very pronounced circular dichroism (CD) in the visible spectral range. As expected, the CD signal switches sign, when the handedness of the helices is changed from left to right. The power of the origami method helped us to generate the plasmonic material exactly according to theoretical specifications - helix rise and diameter are rationally designed. The resuiting helices are among the first self-assembled structures to show a non-trivial optical effect based on plasmon interactions. (scale bar in the figure: 20 nm)

Driving biomolecular nanodevices with synthetic in vitro gene circuits: One of the major challenges for synthetic biology is the realization of large biochemical circuits composed of smaller, well-defined functional "modules". Due to the large number of interacting components and potentially detrimental, unintended "feedback loops", connecting several modules together can lead to a severe deterioration of systems performance. We here addressed this problem by studying an in vitro model system. We utilized a synthetic biochemical clock based on in vitro transcription reactions to periodically drive the motion of a DNA nanodevice (the "DNA tweezers"). Using a variety of different "coupling modes" between oscillator circuit and nanodevice, it was indeed possible to control the motion of the tweezers. However, the dynamics of the oscillator were strongly affected, when we increased the "load". We therefore developed an insulator circuit (corresponding to a "buffer amplifier" in electronics) that effectively uncoupled the load from the driving circuit, and therefore reduced undesirable biochemical "back-action".

This work was conducted in collaboration with the Winfree and Murray labs at Caltech.

E. Franco, E. Friedrichs, J. Kim, R. Jungmann, R. Murray, E. Winfree, F. C. Simmel, Timing molecular production and motion with a synthetic transcriptional clock, PNAS 108, E784-E793 (2011). DOI: 10.1073/pnas.1100060108

DNA-PAINT: DNA origami is a powerful method for the programmable assembly of nanoscale molecular structures. For applications of these structures as functional biomaterials, the study of reaction kinetics and dynamic processes in real time and with high spatial resolution becomes increasingly important. We present a single-molecule assay for the study of binding and unbinding kinetics on DNA origami. We find that the kinetics of hybridization to single-stranded extensions on DNA origami is similar to isolated substrate-immobilized DNA with a slight position dependence on the origami. On the basis of the knowledge of the kinetics, we exploit reversible specific binding of labeled oligonucleotides to DNA nanostructures for PAINT (points accumulation for imaging in nanoscale topography) imaging with <30 nm resolution. The method is demonstrated for flat monomeric DNA structures as well as multimeric, ribbon-like DNA structures.

The DNA-PAINT software is available in the software section.