Within a NSFC-DFG funded joint Sino-German collaboration between the group of Jie Song (Shanghai Jiao Tong University & Hangzhou Institute of Medicine) and our group, we investigated the use of circular single-stranded DNA as gene vectors. We found evidence that gene encoding single-strands are… [read more]

Toehold-mediated strand displacement (TMSD) is a key mechanism in DNA nanotechnology, with applications in molecular devices, biosensors, and DNA computing. In this study we explored TMSD kinetics in water-in-oil emulsion droplets using a droplet microfluidic 'stopped flow' set-up, revealing that… [read more]

Adopting architectural elements of naturally occurring riboswitches, fluorescent light-up aptamers such as Spinach can be made responsive to the presence of RNA input molecules and also small molecule ligands such as guanine or adenine. In the absence of input triggers, the FLAPs display a very low… [read more]

In this paper, surface display of a streptavidin binding peptide is utilized for the massively parallel screening of a riboswitch sequence library via magnetic bead selection: L. Givelet, A. Bienau, F. C. Simmel, A Massively Parallel Double‐Selection Workflow for the Evolution of Molecular Switches… [read more]

Toehold-mediated strand displacement (TMSD) - one of the most applied reactions of dynamic DNA nanotechnology - involves the displacement of an "incumbent" strand bound to a complementary strand by an "invader" strand, which is supported by a short, single-stranded sequence - the toehold - to which… [read more]

The results of a long-term collaboration with our former visiting professors Pekka Orponen (Aalto University) and Ibuki Kawamata (Tohoku University), and with Anton Kuzyk (Aalto University) as the experimental lead finally got published! The idea behind the paper is that the spanning tree of a… [read more]

Due to the exhaustion of cell-free gene expression systems over time, it is difficult to realize cell-free gene circuits in closed reactors that require extended runtimes for operation. In this work we show that execution of an incoherent feed-forward loop of type 2 (IFFL-2)  - capable of… [read more]

We are happy to announce that Lukas Oesinghaus received one of the prestigious Dimitris N. Chorafas prizes for his excellent PhD thesis and related publications. Congratulations! The Dimitris N. Chorafas Foundation awards scientific prizes for outstanding work in selected fields in the engineering… [read more]

Work initiated during the iGEM project Phactory (2018) has now resulted in a publication on the cell-free production of bacteriophages against multidrug-resistent bacteria. The work was performed by Quirin and Kilian from the original team and Gil Westmeyer (TUM Chemistry/Helmholtz) led the… [read more]

Periodic perturbation or driving of nonlinear oscillators is known to lead to complex dynamics such as period doubling bifurcations or even chaos. In the context of biochemical and biological oscillators, this phenomenon has been predicted, but is difficult to observe experimentally. Here, we… [read more]

Combining the switching principle of riboswitches with that of toehold switches, Tianhe (Mark) Wang created a series of novel translational and transcriptional gene regulators, including the first synthetic switch utilizing Rho-dependent termination. Read the full story in Nucleic Acids Research: … [read more]

A study of this effect by Elisabeth Falgenhauer, Andrea Mückl and Matthaeus Schwarz-Schilling has just been published: Falgenhauer, E., Mückl, A., Schwarz-Schilling, M. & Simmel, F. C. Transcriptional Interference in Toehold Switch-Based RNA Circuits. ACS Synth Biol (2022)… [read more]

now published in ACS Applied Materials & Interfaces: [read more]

just accepted in ChemElectroChem: ChemElectroChem2022, e202101696 https://doi.org/10.1002/celc.202101696 [read more]

Successful PhD Defenses in 2022: Julia Müller (14.01.) [read more]

Elisabeth's paper just went online: Falgenhauer, E., von Schönberg, S., Meng, C., Mückl, A., Vogele, K., Emslander, Q., Ludwig, C. and Simmel, F..C. (2021), Evaluation of an E. coli cell extract prepared by lysozyme-assisted sonication via gene expression, phage assembly and proteomics.… [read more]

Successful PhD Defenses in 2021: Marisa Götzfried (22.01.) Andrea Meyer (29.01.) John Henningsen (17.12.) [read more]

Successful PhD defenses in 2020: Kilian Vogele (15.09.) Ali Aghebat Rafat (13.11.) Daniela Ziegler (17.12.) [read more]

Publication: Henningsen, J., Schwarz-Schilling, M., Leibl, A., Gutiérrez, J. N., Sagredo, S., & Simmel, F. C. (2020). Single Cell Characterization of a Synthetic Bacterial Clock with a Hybrid Feedback Loop Containing dCas9-sgRNA. ACS Synthetic Biology, 9(12), 3377–3387 … [read more]

Publication: Frank, T., Vogele, K., Dupin, A., Simmel, F. C., & Pirzer, T. (2020). Growth of Giant Peptide Vesicles Driven by Compartmentalized Transcription-Translation Activity. Chemistry Eur. J., 26(72), 17356–17360. http://doi.org/10.1002/chem.202003366 [read more]

Successful PhD defenses in 2019: Martin Langecker (22.03.) Enzo Kopperger (24.05.) Matthaeus Schwarz-Schilling (16.07.) Aurore Dupin (31.10.) [read more]

Publication: M. A. Goetzfried, K. Vogele, A. Mückl, M. Kaiser, N. B. Holland, F. C. Simmel, T. Pirzer, Periodic Operation of a Dynamic DNA Origami Structure Utilizing the Hydrophilic–Hydrophobic Phase-Transition of Stimulus-Sensitive Polypeptides, Small, 1903541 (2019). … [read more]

 F. C. Simmel, B. Yurke, H. Singh: Principles and applications of nucleic acid strand displacement reactions, Chemical Reviews, Article ASAP(2019). DOI: 10.1021/acs.chemrev.8b00580 (2019) [read more]

Using water-in-oil droplets, we have created two-dimensional networks of artificial cells separated by lipid bilayer interfaces. Within this "micro-tissue" the cells can communicate via the exchange of small molecule signals. Coupling these signals to cell-free genetic feedback and feedforward… [read more]

K. Vogele, J. List, F. C. Simmel, T. Pirzer Langmuir (2018). This article is part of the Nucleic Acids Nanoscience at Interfaces special issue. DOI: 10.1021/acs.langmuir.8b01770 [read more]

L. Aufinger, F. C. Simmel Angew. Chem. Int. Ed. 57, published online (2018) DOI: 10.1002/anie.201809374 [read more]

In a Chinese-German collaboration with Chunhai Fan, Huajie Liu and coworkers, localized DNA strand displacement cascades were realized that allow exploration of paths in tree-like graphs defined on the origami platforms. Read the full story here: J. Chao, J. Wang, F. Wang, X. Ouyang, E.… [read more]

This years iGEM team Munich, hosted by the Simmel lab, wins multiple trophies in the overgraduate section at the iGEM giant jamboree: "Best Manufacturing Project", "Best Presentation", "Best Wiki", "Best Software Tool", "Best Entrepreneurship" and last but not least 1st Runner Up Overgrad (out of… [read more]

G. Pardatscher*, M. Schwarz-Schilling*, S. Sagredo, F. C. SimmelJ. Vis. Exp. (140), e58634, (2018)DOI: 10.3791/58634 [read more]

K. Vogele, T. Frank, L. Gasser, M. A. Goetzfried, M. W. Hackl, S. A. Sieber, F. C. Simmel, and Tobias PirzerNature Communications 9, 3862:1–7 (2018)DOI: 10.1038/s41467-018-06379-8 [read more]

A. Mückl*, M. Schwarz-Schilling*, K. Fischer, and F. C. SimmelPLOS ONE, 13(9): e0198058 (2018)DOI: 10.1371/journal.pone.0198058 [read more]

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The international Genetically Engineered Machine (iGEM) Competition is the biggest synthetic biology student competition in the world with over 300 teams from 44 countries. Following last year's success, the Simmel lab is again supervising a team of highly motivated students who work on a… [read more]

M. Schwarz-Schilling, A. Dupin, F. Chizzolini, S. Krishnan, S. S. Mansy, and F. C. SimmelNano Letters 18, 2650–2657 (2018)DOI: 10.1021/acs.nanolett.8b00526 [read more]

Perspective article by Björn Högberg: Remote control of nanoscale devices http://science.sciencemag.org/content/359/6373/279 Cover of Science Vol 359, Issue 6373: http://science.sciencemag.org/content/359/6373 Animated video: https://youtu.be/K9fuSVaszyg [read more]

After developing their interdisciplinary diagnostics project over the summer in the laboratory of Prof. Dr. Friedrich Simmel, the Munich team (TUM and LMU) was awarded the 1st Runner Up Prize of the "Overgraduate" section. Furthermore, it received special awards in the categories "Best Diagnostics… [read more]

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Cover of Nature Nanotechnology (December 2016). Link Image of the month by 'Wired UK' (02/17) Ten years in images (Nature Nanotechnology anniversary feature). DOI: 10.1038/nnano.2016.190 Image of the month by 'Spektrum der Wissenschaft' (October 2016). Link Images of the month by 'nature.com'… [read more]

K. Vogele, J. List, G. Pardatscher, N. B. Holland, F. C. Simmel, and T. Pirzer DOI: 10.1021/acsnano.6b06635 [read more]

bpod.mrc.ac.uk/archive/2016/10/29 [read more]

Swati Krishnan, Daniela Ziegler, Vera Arnaut, Thomas G. Martin, Korbinian Kapsner, Katharina Henneberg, Andreas R. Bausch, Hendrik Dietz & Friedrich C. Simmel DOI:10.1038/ncomms12787 [read more]

“The DNA Computing Scientist 2016” goes to Friedrich Simmel for his contributions in advancing DNA based networks and self-organization of DNA-based systems. isnsce.org/2016/10/05/award-winners-at-dna22/ [read more]

Aradhana Chopra, Swati Krishnan, and Friedrich C. Simmel DOI: 10.1021/acs.nanolett.6b03586 [read more]

Normally, individual molecules of genetic material repel each other. However, when space is limited DNA molecules must be packed together more tightly. This case arises in sperm, cell nuclei and the protein shells of viruses. An international team of physicists has now succeeded in artificially… [read more]