GRK  2062 "Molecular Principles of Synthetic Biology"

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Gartner, FM., Graf, IR., Wilke, P., Geiger, PM., Frey, E. (2020). Stochastic yield catastrophes and robustness in self-assembly. Elife, 2020(9)

Miermans, CA., Broedersz, CP. (2020). A lattice kinetic Monte-Carlo method for simulating chromosomal dynamics and other (non-)equilibrium bio assemblies. Soft Matter, 16(2), 544-556

Pinheiro, B., Petrov, D.P., Martins, H.B., Bramkamp, M., Jung, K. (2020) Elongation factor P is required for EIIGlc translation in Corynebacterium glutamicum due to an essential polyproline motif. Mol. Microbiol., Online ahead of print.

Pinheiro, B., Scheidler, CM., Kielkowski, P., Schmid, M., Forné, I., Ye, S., Reiling, N., Takano, E., Imhof, A., Sieber, SA., Schneider, S., Jung, K. (2020). Structure and Function of an Elongation Factor P Subfamily in Actinobacteria. Cell Rep, 30(13), 4332-4342

Sommer, CA., Eichinger, A., Skerra, A. (2020). A Tetrahedral Boronic Acid Diester Formed by an Unnatural Amino Acid in the Ligand Pocket of an Engineered Lipocalin. Chembiochem, 21(4), 469-472

Wigbers, MC., Brauns, F., Hermann, T., Frey, E. (2020). Pattern localization to a domain edge. Phys Rev E, 101(2-1), 022414


Becker, S., Feldmann, J., Wiedemann, S., Okamura, H., Schneider, C., Iwan, K., Crisp, A., Rossa, M., Amatov, T., and Carell, T. (2019). Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides. Science 366, 76-82.

Brameyer, S., Rösch, T.C., El Andari, J., Hoyer, E., Schwarz, J., Graumann, P.L., and Jung, K. (2019). DNA-binding directs the localization of a membrane-integrated receptor of the ToxR family. Commun Biol 2, 4.

de Boer, M., Gouridis, G., Vietrov, R., Begg, S.L., Schuurman-Wolters, G.K., Husada, F., Eleftheriadis, N., Poolman, B., McDevitt, C.A., and Cordes, T. (2019). Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers. eLife 8, e44652.

Dann, M., and Leister, D. (2019). Evidence that cyanobacterial Sll1217 functions analogously to PGRL1 in enhancing PGR5-dependent cyclic electron flow. Nat Commun 10, 5299.

Dupin, A., and Simmel, F.C. (2019). Signalling and differentiation in emulsion-based multi-compartmentalized in vitro gene circuits. Nat Chem 11, 32-39.

Glock, P., Brauns, F., Halatek, J., Frey, E., and Schwille, P. (2019). Design of biochemical pattern forming systems from minimal motifs. eLife 8, e48646.

Glock, P., Ramm, B., Heermann, T., Kretschmer, S., Schweizer, J., Mücksch, J., Alagöz, G., and Schwille, P. (2019). Stationary patterns in a two-protein reaction-diffusion system. ACS Synth Biol 2018.

Hürtgen, D.*, Härtel, T.*, Murray, S.M., Sourjik, V., and Schwille, P. (* contributed equally) (2019). Functional modules of minimal cell division for synthetic biology. Adv Biosyst 2019, 1800315.

Jung, K., Brameyer, S., Fabiani, F., Gasperotti, A., and Hoyer, E. (2019). Phenotypic heterogeneity generated by histidine kinase-based signaling networks. J Mol Biol, Apr 7. pii: S0022-2836(19)30184-6. [Epub ahead of print]

Mächtel, R., Narducci, A., Griffith, D.A., Cordes, T., and Orelle, C. (2019). An integrated transport mechanism of the maltose ABC importer. Res Microbiol 170, 321-337.

Miermans, C.A., and Broedersz, C.P. (2019). Lattice kinetic Monte-Carlo method for simulating chromosomal dynamics and other (non-)equilibrium bio-assemblies. Soft Matter 2019, accepted manuscript.

Peschek, N., Hoyos, M., Herzog, R., Förstner, K.U., and Papenfort, K. (2019). A conserved RNA seed-pairing domain directs small RNA-mediated stress resistance in enterobacteria. EMBO J 38, e101650.

Scheidler, C.M., Kick, L.M., and Schneider, S. (2019). Ribosomal peptides and small proteins on the rise. ChemBioChem

Volkwein, W., Krafczyk, R., Jagtap, P.K.A., Parr, M., Mankina, E., Macošek, J., Guo, Z.,Fürst, M.J., Pfab, M., Frishman, D., Hennig, J., Jung, K., and Lassak, J. (2019). Switching the post-translational modification of translation elongation factor EF P. Front Microbiol 10.


Baumann, A., Marchner, S., Daum, M., and Hoffmann-Röder, A. (2018). Synthesis of fluorinated Leishmania cap trisaccharides for diagnostic tool and vaccine development. Eur J Org Chem 2018, 3803-3815.

Carell, T., Kurz, M.Q., Müller, M., Rossa, M., and Spada, F. (2018). Non-canonical bases in the genome: the regulatory information layer in DNA. Angew Chem Int Ed Engl 57, 4296–4312.

Glock, P., Broichhagen, J., Kretschmer, S., Blumhardt, P., Mücksch, J., Trauner, D., and Schwille, P. (2018). Optical control of a biological reaction-diffusion system. Angew Chem Int Ed Engl 57, 2362–2366.

Glock, P. and Schwille, P. (2018). Switching protein patterns on membranes. Curr Opin Colloid Interface Sci 38, 100–107.

Halatek, J., Brauns, F., and Frey, E. (2018). Self-organisation principles of intracellular pattern formation. Phil Trans R Soc B 373, 20170107.

Herzog, R., and Papenfort, K. (2018) Chapter thirteen - Transcriptomic approaches for studying quorum sensing in Vibrio cholerae. In: Methods in Enzymology 612, 303-342.

Jia, H., Kai, L., Heymann, M., García-Soriano, D.A., Härtel, T., and Schwille, P. (2018). Light-induced printing of protein structures on membranes in vitro. Nano Lett 18, 7133-7140.

Jung, K., Fabiani, F., Hoyer, E., and Lassak, J. (2018). Bacterial transmembrane signalling systems and their engineering for biosensing. Open Biol 8, 180023.

Leister, D. (2018). Genetic engineering, synthetic biology and the light reactions of photosynthesis. Plant Physiol, pp.00360.02018.

Leister, D. (2018). Thawing out frozen metabolic accidents. BMC Biol 17, 8.

Lerner, E., Cordes, T., Ingargiola, A., Alhadid, Y., Chung, S., Michalet, X., and Weiss, S. (2018). Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 359, eaan1133.

Litschel, T., Ganzinger, K., Movinkel, T., Heymann, M., Robinson, T., Mutschler, H., and Schwille, P. (2018). Optimizing content mixing of protocell models in freeze-thaw cycles. New J Phys 20, 055008.

Litschel, T., Ramm, B., Mass, R., Heymann, M., and Schwille, P. (2018). Beating vesicles: Encapsulated protein oscillations cause dynamic membrane deformations. Angew Chem Int Ed 57, 16286-16290.

Miermans, C.A., and Broedersz, C.P. (2018). Bacterial chromosome organization by collective dynamics of SMC condensins. J Royal Soc Interface 15, 20180495.

Mückl, A., Schwarz-Schilling, M., Fischer, K., and Simmel, F.C. (2018). Filamentation and restoration of normal growth in Escherichia coli using a combined CRISPRi sgRNA/antisense RNA approach. PLoS One 13, e0198058.

Niederauer, C., Blumhardt, P., Mücksch, J., Heymann, M., Lambacher, A., and Schwille P., (2018). Direct characterization of the evanescent field in objective-type total internal reflection microscopy. Opt Express 26, 20492-20506.

Pardatscher, G.*, Schwarz-Schilling, M.*, Sagredo, S., and Simmel, F.C. (2018). Functional surface-immobilization of genes using multistep strand displacement lithography. *Shared authorship. J Vis Exp 140, e58634.

Pardatscher, G., Schwarz-Schilling, M., Daube, S.S., Bar-Ziv, R.H., and Simmel, F.C. (2018). Gene expression on DNA biochips patterned with strand-displacement lithography. Angew Chem Int Ed 57, 4783-4786

Ramm B, Glock P, and Schwille P. (2018). In vitro reconstitution of self-organizing protein patterns on supported lipid bilayers. J Vis Exp 137, e58139.

Ramm, B., Glock, P., Mücksch, J., Blumhardt, P., Heymann, M., and Schwille, P. (2018). The MinDE system is a generic spatial cue for membrane protein distribution in vitro. Nat Commun 9, 3942.

Schiefner, A., Nästle, L., Landgraf, M., Reichert, A. J., and Skerra, A. (2018). Structural basis for the specific cotranslational incorporation of p-boronophenylalanine into biosynthetic proteins. Biochemistry 57, 2597-2600.

Schwarz-Schilling, M., Dupin, A., Chizzolini, F., Krishnan, S., Mansy, S.S., and Simmel, F.C. (2018). Optimized assembly of a multifunctional RNA-protein nanostructure in a cell-free gene expression system. Nano Lett 18, 2650-2657.

Wilke, P., Reithmann, E., and Frey, E. (2018). Two-species active transport along cylindrical biofilaments is limited by emergent topological hindrance. Phys Rev X 8, 031063.


Dann, M., and Leister, D. (2017). Enhancing (crop) plant photosynthesis by introducing novel genetic diversity. Phil Trans R Soc B 372, 20160380.

Edupuganti, R.R., Geiger, S., Lindeboom, R.G.H., Shi, H., Hsu, P.J., Lu, Z., Wang, S.-Y., Baltissen, M.P.A., Jansen, P.W.T.C., Rossa, M., Müller, M., Stunnenberg, H. G., He, C., Carell, T., and Vermeulen, M. (2017). N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat Struct Mol Biol 24, 870–878.

Edwardraja, S., Eichinger, A., Theobald, I., Sommer, C.A., Reichert, A.J., and Skerra, A. (2017). Rational design of an anticalin-type sugar-binding protein using a genetically encoded boronate side chain. ACS Synth Biol 6, 2241-2247.

Gandini, C., Schmidt, S.B., Husted, S., Schneider, A., and Leister, D. (2017). The transporter SynPAM71 is located in the plasma membrane and thylakoids, and mediates manganese tolerance in Synechocystis PCC6803. New Phytol 215, 256-268.

Gladrow, J., Broedersz, C.P., and Schmidt, C.F. (2017) Nonequilibrium dynamics of probe filaments in actin-myosin networks. Physical  Review E 96, 022408

Jia, H., Heymann, M., Bernhard, F., Schwille, P., and Kai, L. (2017). Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. New Biotechnol 39, 199-205.

Kick, L., Kirchner, M., and Schneider, S. (2017). CRISPR-Cas9: from a bacterial immune system to genome-edited human cells in clinical trials. Bioengineered 8, 280-286.

Kirchner, M., and Schneider, S. (2017). Gene expression control by Bacillus anthracis purine riboswitches. RNA 23, 762-9.

Kirchner, M., Schorpp, K., Hadian, K., and Schneider, S. (2017). An in vivo high-throughput screening for riboswitch ligands using a reverse reporter gene system. Sci Rep 7, 7732.

Kitsera, N., Allgayer, J., Parsa, E., Geier, N., Rossa, M., Carell, T., and Khobta, A. (2017). Functional impacts of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine at a single hemi-modified CpG dinucleotide in a gene promoter. Nucleic Acids Res 45, 11033–11042.

Krafczyk, R., Macošek, J., Jagtap, P.K.A., Gast, D., Wunder, S., Mitra, P., Jha, A.K., Rohr, J., Hoffmann-Röder, A., Jung, K., Hennig, J., and Lassak, J. (2017). Structural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P. mBio 8, e01412-17.

Leister, D. (2017) Experimental evolution in photoautotrophic microorganisms as a means of enhancing chloroplast functions. Essays in Biochem 2017 Sep 7

Paieri, F., Tadini, L., Manavski, N., Kleine, T., Morandini, P., Pesaresi, P., Meurer, J., and Leister, D. (2017). The DEAD-box RNA helicase RH50 is a 23S-4.5S rRNA maturation factor that functionally overlaps with the plastid signaling factor GUN1. Plant Physiol 176, 634–648.

Volkwein, W., Maier, C., Krafczyk, R., Jung, K., and Lassak, J. (2017). A versatile toolbox for the control of protein levels using Nε-acetyl-L-lysine dependent amber suppression, ACS Synth Biol 6, 1892-1902.

Wang, Y., Heermann. R., and Jung, J. (2017) CipA and CipB as scaffolds to organize proteins into crystalline inclusions. ACS Synthetic Biology


Fröhlich, K.S., and Papenfort, K. (2016).  Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens. Mol Microbiol

Fröhlich, K.S., Haneke, K., Papenfort, K., and Vogel, J. (2016). The target spectrum of SdsR small RNA in Salmonella.  Nucl Acids Res

Li, X., Krafczyk, R., Macoşek, J., Li, Y.-L., Zou, Y., Simon, B., Pan, X., Wu, Q.-Y., Yan, F, Li, S., Hennig, J., Jung, K., Lassak, J., and Hu, H.-G. (2016). Resolving the α-glycosidic linkage of arginine-rhamnosylated translation elongation factor P (EF-P) triggers generation of the first ArgRha specific antibody. Chem Sci 7, 6995-7001. 

Schwarz-Schilling, M., Aufinger, L., Muckl, A., and Simmel, F.C. (2016). Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets. Integr Biol 8, 564-570.

Schwarz-Schilling, M., Kim, J., Cuba, C., Weitz, M., Franco, E., and Simmel, F.C. (2016). Building a synthetic transcriptional oscillator. Methods Mol Biol 1342, 185-99.

Wunder, S., Deutsch, A., Deutsch, C., and Hoffmann-Röder, A. (2016). One-pot synthesis of functionalized β-fluoroalkylated Mannich-type products from N-aryl N,O-acetals. Synthesis 48, 1167-1176.


Kirchner, M., and Schneider, S. (2015). CRISPR - Cas: From the bacterial adaptive immune system to a versatile genome engineering toolbox. Angew Chem Int Ed 54, 13508-13514.

Reichert, A.J., Poxleitner, G., Dauner, M. and Skerra, A. (2015). Optimisation of a system for the co-translational incorporation of a keto amino acid and its application to a tumour-specific Anticalin. Protein Eng Des Sel 28, 553-565.