Welcome to the Simmel lab - Physics of Synthetic Biological Systems

Our goal is the realization of self-organizing molecular and cellular 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 and develop.

A Brownian ratchet rotor made from DNA origami: In collaboration with the Dietz group, the first Brownian ratchet based on a DNA origami structure was realized, which displays directional rotational movement due to its intrinsic asymmetry when driven out of thermal equilibrium. The structure consists of an arm sitting on a pedestal with three obstacles, leading to six preferred orientations of the arm. When the structure is actuated with an alternating linear electric field (that is not rotating!), the arm rotates directionally. The behavior of the arm is consistent with a "flashing Brownian ratchet" model. Theoretical support for the investigation of the system was provided by the Golestanian group (MPI DS Göttingen).

A.-K. Pumm, W. Engelen, E. Kopperger, J. Isensee, M. Vogt, V. Kozina, M. Kube, M. N. Honemann, E. Bertosin, M. Langecker, R. Golestanian#, F. C. Simmel#, H. Dietz#, A DNA origami rotary ratchet motor, Nature 607, 492–498 (2022). https://doi.org/10.1038/s41586-022-04910-y

Positional information in synthetic cell assemblies: In biological development, an initially homogeneous “material” differentiates into functionally distinct spatial regions, guided by chemical cues from its environment. How well and how robustly a biological system can infer spatial position from the local concentrations of chemicals can be quantified using the theoretical concept of “positional information”. In our work we applied this concept to synthetic cell assemblies. To this end, we created assemblies containing cell-free gene circuits that responded to morphogen gradients in a position-dependent manner. We found that the systems can differentiate into 2-3 regions, and our theoretical analysis allowed us to investigate the  parameters that determine and limit the capability of the system to differentiate. We anticipate that similar analyses will be crucial for the further development of autonomous “life-like” materials composed of synthetic cells.

A. Dupin*, L. Aufinger*, I. Styazhkin, F. Rothfischer, B. Kaufmann, S. Schwarz, N. Galensowske, H. Clausen-Schaumann, and F. C. Simmel, Synthetic cell-based materials extract positional information from morphogen gradients, Sci. Adv. 8, eabl9228 (2022).

Electrically driven colloidal pattern formation: It has long been known that aqueous colloidal suspensions subjected to time-varying electrical fields form intriguing spatial patterns - they align into chains and then form distinct zigzag band patterns, which are tilted with respect to the electric field direction. In the present work, we demonstrate that the patterns arise with a wide range of different colloidal suspensions (silica particles, droplets, coacervates, bacteria, coffee!) and give a theoretical explanation based on hydrodynamic interactions caused by the electrokinetic flow around the particles.

F. Katzmeier, B. Altaner, J. List, U. Gerland, and F.C. Simmel, Emergence of Colloidal Patterns in ac Electric Fields, Phys. Rev. Lett. 128, 058002 (2022). doi.org/10.1103/PhysRevLett.128.058002

Conditional guide RNAs for Cas12a in mammalian cells: Conditional guide RNAs (gRNAs) allow to make CRISPR-based processes such as gene editing or gene regulation dependent on cellular or environmental signals. We have developed a novel strategy to switch gRNAs for the CRISPR-associated protein Cas12a based on various molecular inputs - microRNAs, short hairpin RNAs, metabolites (via a ribozyme) or other RNA inputs (via a strand displacement process) in mammalian cells. Importantly, in this approach the guide RNAs are produced via a Pol II-promoter and later processed to become a fully functional gRNA. This also allows to encode a full gRNA circuit - including the mRNA encoding the Cas12a - on a single transcript.

L. Oesinghaus and F.C. Simmel, Controlling Gene Expression in Mammalian Cells Using Multiplexed Conditional Guide RNAs for Cas12a, Angew. Chem. Int. Ed. (2021). https://doi.org/10.1002/anie.202107258

Multi-aptamer scaffolds: Aptamers provide a “natural” interface between the DNA and protein world, and have been previously used to bind and arrange proteins on DNA nanostructures. Multivalent binding of target proteins by several aptamers is known to improve the binding strength, but the full potential of origami nanostructures to control the orientation of multiple binders, and also to adjust the flexibility of the binders to enhance their binding properties, has not been utilized so far. We now demonstrate a multiplexed single molecule assay based on DNA origami cavities to optimize the influence of geometry and molecular mechanical properties in two model protein-aptamer systems. Maybe most interestingly, our work also hints at the possibility to “evolve” DNA origami/aptamer scaffolds in a similar way as the SELEX method is used to evolve aptamers in the first place. As a first step in this direction, we demonstrate affinity selection of good binders from a mixture of origami structures. 

A. Aghebat Rafat*, S. Sagredo*, M. Thalhammer & F. C. Simmel, Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities, Nature Chemistry 12, 852-859 (2020). doi:10.1038/s41557-020-0504-6

3D printing meets dynamic DNA nanotechnology: Additive manufacturing enables the generation of 3D structures with defined shapes from a wide range of printable materials. Most of the materials employed so far are static and do not provide any intrinsic programma-bility or pattern-forming capability. On the other hand, the exquisite programmability of DNA-based systems has only rarely been used to generate functional materials on the mm-scale and above. In order to bring together “the best of both worlds”, we developed a low-cost 3D bioprinting approach using a DNA-functionalized bioink. We show that dynamic DNA nanotechnology can be used to control diffusion, addressable localization, and pattern formation in 3D printed gels.

J. Müller, A.C. Jäkel, D. Schwarz, L. Aufinger, F.C. Simmel, Programming Diffusion and Localization of DNA Signals in 3D-Printed DNA-Functionalized Hydrogels, Small 347, 2001815–10 (2020).

Multi-input logic for CRISPR-Cas12a: CRISPR mechanisms utilize the action of RNA-dependent nucleases  to bind to and process DNA molecules whose sequence is determined by so-called guide RNAs (gRNAs), which make them natural candidates for regulation by RNA strand displacement processes. In this work, we utilized the intrinsic gRNA processing property of the CRISPR-associated protein Cas12a to implement guide RNAs that are switchable by RNA strand displacement reactions. Inactive strand-displacement gRNAs (SDgRNAs) can be activated by trigger RNA molecules, which induce a conformational change that facilitates binding of Cas12a. After processing of the SDgRNA, the resulting Cas12a-gRNA is fully active. Using this switchable principle, we demonstrate control of DNA processing by Cas12a in vitro via RNA-based input logic circuits. Using the catalytically inactive mutant dCas12a, we also realize SDgRNA-based logical control of gene expression in E.coli bacteria.

L. Oesinghaus, F. C. Simmel, Switching the activity of Cas12a using guide RNA strand displacement circuits, Nature Communications (2019). DOI: 10.1038/s41467-019-09953-w

Communicating artificial cells: Multicellularity in living organisms allows for complex behavior through differentiation of cell types. We have assembled artificial cells into synthetic "microtissues” through the use of water-in-oil droplets forming lipid bilayers upon contact with each other. We established and characterized cell-to-cell communication in these artificial multicellular structures. Using different types of synthetic in vitro gene circuits, we then implemented two examples of more complex dynamical behavior in such systems: spatial propagation of a chemical signal and a simple form of cellular differentiation.

A. Dupin, F. C. Simmel, Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat Chem. 11, 32–39 (2019). https://www.nature.com/articles/s41557-018-0174-9

News and Views article by Li & Schulman: https://doi.org/10.1038/s41557-018-0192-7