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Amorphous and Evolutionary DNA Nanotechnology

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Publications

Establishing Communication Between Artificial Cells

Author(s): Lukas Aufinger, Friedrich C. Simmel
Published in: Chemistry – A European Journal, 25/55, 2019, Page(s) 12659-12670, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201901726

Bacterial Growth, Communication, and Guided Chemotaxis in 3D-Bioprinted Hydrogel Environments

Author(s): Julia Müller, Anna C. Jäkel, Jonathan Richter, Markus Eder, Elisabeth Falgenhauer, and Friedrich C. Simmel
Published in: ACS Applied Materials and Interfaces, 2022, ISSN 1944-8244
Publisher: American Chemical Society
DOI: 10.1021/acsami.1c20836

Genetically Encoded Membranes for Bottom‐Up Biology

Author(s): Kilian Vogele, Tobias Pirzer, Friedrich C. Simmel
Published in: ChemSystemsChem, 1/4, 2019, ISSN 2570-4206
Publisher: Wiley-VCH
DOI: 10.1002/syst.201900016

Single Cell Characterization of a Synthetic Bacterial Clock with a Hybrid Feedback Loop Containing dCas9-sgRNA

Author(s): John Henningsen, Matthaeus Schwarz-Schilling, Andreas Leibl, Joaquı́n Gutiérrez, Sandra Sagredo, and Friedrich C. Simmel
Published in: ACS Synthetic BIology, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00438

Programming Diffusion and Localization of DNA Signals in 3D‐Printed DNA‐Functionalized Hydrogels

Author(s): Julia Müller, Anna Christina Jäkel, Dominic Schwarz, Lukas Aufinger, Friedrich C. Simmel
Published in: Small, 16/31, 2020, Page(s) 2001815, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.202001815

Single DNA Origami Detection by Nanoimpact Electrochemistry

Author(s): Evangelina Pensa, Yash Bogawat, Friedrich C. Simmel, Ibon Santiago
Published in: ChemElectroChem, 2022, ISSN 2196-0216
Publisher: Wiley-VCH
DOI: 10.1002/celc.202101696

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a

Author(s): Florian Katzmeier, Lukas Aufinger, Aurore Dupin, Jorge Quintero, Matthias Lenz, Ludwig Bauer, Sven Klumpe, Dawafuti Sherpa, Benedikt Dürr, Maximilian Honemann, Igor Styazhkin, Friedrich C. Simmel, Michael Heymann
Published in: PLOS ONE, 14/12, 2019, Page(s) e0220091, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0220091

Emergence of Colloidal Patterns in ac Electric Fields

Author(s): Florian Katzmeier, Bernhard Altaner, Jonathan List, Ulrich Gerland, and Friedrich C. Simmel
Published in: Physical Review Letters, 2022, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.128.058002

Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities

Author(s): Ali Aghebat Rafat, Sandra Sagredo, Melissa Thalhammer, Friedrich C. Simmel
Published in: Nature Chemistry, 12/9, 2020, Page(s) 852-859, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-020-0504-6

Synthetic cell–based materials extract positional information from morphogen gradients

Author(s): Aurore Dupin, Lukas Aufinger, Igor Styazhkin, Florian Rothfischer, Benedikt K. Kaufmann, Sascha Schwarz, Nikolas Galensowske, Hauke Clausen-Schaumann, Friedrich C. Simmel
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1126/sciadv.abl9228

Growth of Giant Peptide Vesicles Driven by Compartmentalized Transcription–Translation Activity

Author(s): Thomas Frank, Kilian Vogele, Aurore Dupin, Friedrich C. Simmel, Tobias Pirzer
Published in: Chemistry – A European Journal, 26/72, 2020, Page(s) 17356-17360, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202003366

Transcriptional Interference in Toehold Switch-Based RNA Circuits

Author(s): Elisabeth Falgenhauer, Andrea Mückl, Matthaeus Schwarz-Schilling, and Friedrich C. Simmel
Published in: ACS Synthetic Biology, 2022, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00486

Self-organizing materials built with DNA

Author(s): Friedrich C. Simmel, Rebecca Schulman
Published in: MRS Bulletin, 42/12, 2017, Page(s) 913-919, ISSN 0883-7694
Publisher: Materials Research Society
DOI: 10.1557/mrs.2017.271

A DNA Nanorobot Uprises against Cancer

Author(s): Hari R. Singh, Enzo Kopperger, Friedrich C. Simmel
Published in: Trends in Molecular Medicine, 24/7, 2018, Page(s) 591-593, ISSN 1471-4914
Publisher: Elsevier BV
DOI: 10.1016/j.molmed.2018.05.001

Artificial Gel-Based Organelles for Spatial Organization of Cell-Free Gene Expression Reactions

Author(s): Lukas Aufinger, Friedrich C. Simmel
Published in: Angewandte Chemie International Edition, 57/52, 2018, Page(s) 17245-17248, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201809374

Towards synthetic cells using peptide-based reaction compartments

Author(s): Kilian Vogele, Thomas Frank, Lukas Gasser, Marisa A. Goetzfried, Mathias W. Hackl, Stephan A. Sieber, Friedrich C. Simmel, Tobias Pirzer
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-06379-8

Functional Surface-immobilization of Genes Using Multistep Strand Displacement Lithography

Author(s): Günther Pardatscher, Matthaeus Schwarz-Schilling, Sandra Sagredo, Friedrich C. Simmel
Published in: Journal of Visualized Experiments, 140, 2018, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/58634

Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits

Author(s): Aurore Dupin, Friedrich C. Simmel
Published in: Nature Chemistry, 11/1, 2019, Page(s) 32-39, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-018-0174-9

Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

Author(s): Aradhana Chopra, Sandra Sagredo, Guido Grossi, Ebbe Andersen, Friedrich Simmel
Published in: Nanomaterials, 9/4, 2019, Page(s) 507, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano9040507

Switching the activity of Cas12a using guide RNA strand displacement circuits

Author(s): Lukas Oesinghaus, Friedrich C. Simmel
Published in: Nature Communications, 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-09953-w

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Author(s): Friedrich C. Simmel, Bernard Yurke, Hari R. Singh
Published in: Chemical Reviews, 119, 2019, Page(s) 6326-6369, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.8b00580

Controlling Chirality across Length Scales using DNA

Author(s): Alessandro Cecconello, Friedrich C. Simmel
Published in: Small, 15, 2019, Page(s) 1805419, ISSN 1613-6810
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/smll.201805419

Controlling gene expression in mammalian cells using multiplexed conditional guide RNAs for Cas12a

Author(s): Lukas Oesinghaus; Friedrich C. Simmel
Published in: Angewandte Chemie Int. Ed., 60, 2021, Page(s) 23894-23902, ISSN 0044-8249
Publisher: Wiley-VCH
DOI: 10.1101/2021.04.16.440136

Small Antisense DNA-Based Gene Silencing Enables Cell-Free Bacteriophage Manipulation and Genome Replication

Author(s): Kilian Vogele, Elisabeth Falgenhauer, Sophie von Schönberg, Friedrich C. Simmel, Tobias Pirzer
Published in: ACS Synthetic Biology, 10/3, 2021, Page(s) 459-465, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00402

Evaluation of an E. coli cell extract prepared by lysozyme‐assisted sonication via gene expression, phage assembly and proteomics

Author(s): Elisabeth Falgenhauer, Sophie von Schönberg, Chen Meng, Andrea Mückl, Kilian Vogele, Quirin Emslander, Christina Ludwig, Friedrich Christian Simmel
Published in: ChemBioChem, 2021, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202100257