Recent Publications

2016

K. Vogele, J. List, G. Pardatscher, N. B. Holland, F. C. Simmel, and T. Pirzer, A Self-Assembled Active Plasmonic Waveguide with a Peptide-Based Thermo-Mechanical Switch, ACS Nano, ASAP(2016) DOI: 10.1021/acsnano.6b06635

S. Krishnan, D. Ziegler, V. Arnaut, T. G. Martin, K. Kapsner, K. Henneberg, A. R. Bausch, H. Dietz, F. C. Simmel, Molecular transport through large-diameter DNA nanopores, Nature Communications 7:12787 (2016). DOI: 10.1038/ncomms12787

A. Chopra, S. Krishnan, F. C. Simmel, Electrotransfection of polyamine folded DNA origami structures, Nano Letters 16 (10), 6683–6690 (2016). DOI: 10.1021/acs.nanolett.6b03586

G. Pardatscher, D. Bracha, O. Vonshak, S. S. Daube, F. C. Simmel, R. H. Bar-Ziv, DNA condensation in one dimension, Nature Nanotechnology 11,1076–1081 (2016). DOI: 10.1038/nnano.2016.142

J. List, E. Falgenhauer, E. Kopperger, G. Pardatscher, F. C. Simmel, Long-Range Movement of Large Mechanically Interlocked DNA Nanostructures, Nature Communications 7:12414 (2016). DOI: 10.1038/ncomms12414

S. Sagredo, T. Pirzer,  A. Aghebat Rafat, M. A. Götzfried, G. Moncalian, F. C. Simmel, F. de la Cruz,  Orthogonal protein assembly on DNA nanostructures using relaxases, Angewandte Chemie Int. Ed. 55, 4348-4352 (2016), DOI: 10.1002/anie.201510313

M. Schwarz-Schilling, L. Aufinger, A. Mückl, F. C. Simmel, Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets, Integrative Biology 8, 564-570 (2016), DOI: 10.1039/C5IB00301F

T. Ramalho, A. Meyer, A. Mückl, K. Kapsner, U. Gerland, F. C. Simmel, Single cell analysis of a bacterial sender-receiver system, PLOS ONE, e0145829 (2016), DOI:10.1371/journal.pone.0145829

2015

M. B. Scheible, L. Ong, J. Woehrstein, R. Jungmann, P. Yin, F. C. Simmel, A compact DNA cube with side length 10 nm, Small 11, 5200–5205 (2015). DOI: 10.1002/smll.201501370

M. Amos, I. M. Axmann, N. Blüthgen, F. de la Cruz, A. Jaramillo, A. Rodriguez-Paton, F. Simmel, Bacterial computing with engineered populations, Philosophical Transactions of the Royal Society of London A 373 (2015). DOI: 10.1098/rsta.2014.0218.

K.Kapsner and F. C. Simmel, Partitioning variability of a compartmentalized in vitro transcriptional thresholding circuit, ACS Synthetic Biology 4, 1136-1143(2015). DOI: 10.1021/acssynbio.5b00051.

E. Kopperger, T. Pirzer, F. C. Simmel, Diffusive transport of molecular cargo tethered to a DNA origami platform, Nano Letters 15, 2693–2699 (2015). DOI: 10.1021/acs.nanolett.5b00351.

S. Kocabey, S. Kempter, J. List, Y. Xing, W. Bae, D. Schiffels, W. Shih, F. C. Simmel, and T. Liedl, Membrane-Assisted Growth of DNA Origami Nanostructure Arrays, ACS Nano 9, 3530–3539 (2015). DOI: 10.1021/acsnano.5b00161.

M. Langecker, A. Ivankin, S. Carson, S. R. M. Kinney, F. C. Simmel, M. Wanunu, Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability, Nano Letters 15, 783-790 (2015).  DOI: 10.1021/nl504522n.

S. Krishnan, F. C. Simmel, Deadly DNA (N & V article), Nature Chemistry 7, 17-18 (2015).

2014

M. Teichmann, E. Kopperger, F. C. Simmel, Robustness of Localized DNA Strand Displacement Cascades, ACS Nano 8, 8487-8496 (2014). DOI: 10.1021/nn503073p

A. Aghebat Rafat, T. Pirzer, M. Scheible, A. Kostina, F. C. Simmel, Surface-Assisted Large-Scale Ordering of DNA Origami Tiles, Angewandte Chemie Int. Ed. 53, 7665-7668 (2014).

M. Langecker, V. Arnaut, J. List, and F. C. Simmel, DNA nanostructures interacting with lipid bilayer membranes, Accounts of Chemical Research 47, 1807-1815 (2014).

J. List, M. Weber, F. C. Simmel, Hydrophobic Actuation of a DNA Origami Bilayer Structure, Angewandte Chemie Int. Ed. 53, 4236-4239 (2014).

M. Weitz, J. Kim, K. Kapsner, E. Winfree, E. Franco, F. C. Simmel, Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator, Nature Chemistry 6, 295-302 (2014). http://dx.doi.org/10.1038/nchem.1869

M. Scheible, G. Pardatscher, A. Kuzyk, F. C. Simmel, Single Molecule Characterization of DNA Binding and Strand Displacement Reactions on Lithographic DNA Origami Microarrays, Nano Letters 14, 1627-1633 (2014).

M. Weitz, A. Mückl, K. Kapsner, R. Berg, A. Meyer, F. C. Simmel, Communication and computation by bacteria compartmentalized within microemulsion droplets, Journal of the American Chemical Society 136, 72-75 (2014).

2013

V. Arnaut, M. Langecker, F. C. Simmel, Nanopore force spectroscopy of aptamer-ligand complexes, Biophysical Journal 105, 1199-1207 (2013).

F. C. Simmel, Artificial cells: Crowded genes perform differently (News & Views article), Nature Nanotechnology 8, 545-546 (2013).

F. C. Simmel, DNA-Nanotechnologie (in German), Chemie in unserer Zeit 47, 164-173 (2013).

C. Troiber, J. C. Kasper, S. Milani, M. Scheible, I. Martin, F. Schaubhut, S. Küchler, J. Rädler, F. C. Simmel, W. Friess, and E. Wagner,  Comparison of four different particle sizing methods for siRNA polyplex characterization, European Journal of Pharmaceutics and Biopharmaceutics 84 (2), 255 (2013).

F. C. Simmel, DNA origami – art, science, and engineering, Frontiers in Life Science (2013). http://dx.doi.org/10.1080/21553769.2012.745453

F. C. Simmel, Programming the dynamics of biochemical reaction networks, ACS Nano 7, 6-10 (2013). http://dx.doi.org/10.1021/nn305811d

2012

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).

F. C. Simmel, DNA-based assembly lines and nanofactories, Curr. Op. Biotechnology 23, 516-521 (2012).

G. P. Acuna, M. Bucher, I. Stein, C. Steinhauer, A. Kuzyk, P. Holzmeister, R. Schreiber, A. Moroz, F. D. Stefani,  T. Liedl, F. C. Simmel, and P. Tinnefeld, Distance dependence of single-fluorophore quenching by gold nanoparticles studied on DNA origami, ACS Nano 6, 3189 - 3195 (2012).

A. Bessonov, J. Takemoto, F. C. Simmel, Probing DNA-lipid membrane interactions with a lipopeptide nanopore, ACS Nano 6, 3356-3363 (2012).

M. Weitz, F. C. Simmel, Synthetic in vitro transcription circuits, Transcription 3, 87-91(2012).

A. Kuzyk, R. Schreiber, Z. Fan, G. Pardatscher, E. Roller, A. Högele, F. C. Simmel, A. Govorov, T. Liedl, DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response, Nature 483, 311-314 (2012).

S. Schink, S. Renner, K. Alim, V. Arnaut, F. C. Simmel, U. Gerland, A versatile first passage framework for the translocation dynamics of structured polynucleotides, Biophysical Journal 102, 85-95 (2012).

R. Jungmann, M. Scheible, F. C. Simmel, Nanoscale imaging in DNA nanotechnology, WIREs Nanomedicine & Nanobiotechnology 4, 66-81 (2012).

2011

M. Langecker, D. Pedone, F. C. Simmel, U. Rant, Electrophoretic time-of-flight measurements of single DNA molecules with two stacked nanopores, Nano Letters 11, 5002-5007 (2011). http://dx.doi.org/10.1021/nl2030079

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, Proc. Natl. Acad. Sci. U.S.A. 108, E784-E793 (2011). DOI: 10.1073/pnas.1100060108

A. Kuzyk, Dielectrophoresis at the nanoscale, Electrophoresis, 32, 2307, (2011). http://dx.doi.org/10.1002/elps.201100038

R. Jungmann,  M. Scheible, A. Kuzyk,  G. Pardatscher,  C. E. Castro, F. C. Simmel, DNA origami-based nanoribbons: assembly, length distribution, and twist, Nanotechnology, 22, 275301 (2011). http://iopscience.iop.org/0957-4484/22/27/275301

Y. Krishnan and F. C. Simmel, Nucleic acid based molecular devices, Angewandte Chemie Int. Ed. 50, 3124-3156 (2011). http://dx.doi.org/10.1002/anie.200907223 http://dx.doi.org/10.1002/anie.200907223

S. Renner, A. Bessonov, F. C. Simmel, Voltage-controlled insertion of single α-hemolysin and MspA nanopores into lipid bilayer membranes, Appl. Phys. Lett. 98, 083701 (2011). http://dx.doi.org/10.1063/1.3558902

2010

S. Renner, A. Bessonov, U. Gerland, F. C. Simmel, Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy, J. Phys. Cond. Mat. 22, 454119 (2010).

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, F. C. Simmel, Single-Molecule Kinetics and Super-Resolution Microscopy by Fluorescence Imaging of Transient Binding on DNA Origami, Nano Letters 10, 4756-4761 (2010) http://dx.doi.org/10.1021/nl103427w

S. Modi, D. Bhatia, F. C. Simmel, and Y. Krishnan, Structural DNA Nanotechnology: From bases to bricks, from structure to function, Journal of Physical Chemistry Letters 1, 1994-2005 (2010). http://dx.doi.org/10.1021/jz1004957

V. Tejedor, O. Benichou, R. Voituriez, R. Jungmann, F. C. Simmel, C. Selhuber, L. Oddershede, and R. Metzler, Quantitative analysis of single particle trajectories, Biophysical Journal 98, 1364-1372 (2010).

S. Kaniber, M. Brandstetter, F. C. Simmel, I. Carmeli, A. Holleitner, On-Chip Functionalization of Carbon Nanotubes with Photosystem I, Journal of the American Chemical Society 132, 2872-2873 (2010).

S. Renner, S. Geltinger, F. C. Simmel, Nanopore Translocation and Force Spectroscopy Experiments in Microemulsion Droplets, Small, 6, 190-194 (2010). http://dx.doi.org/10.1002/smll.200901435

2009

F. C. Simmel, N & V: Wiring up ion channels, Nature Physics 5, 783 - 784 (2009).

C. Steinhauer, R. Jungmann, T. Sobey, F. C. Simmel, P. Tinnefeld, DNA Origami as a Nanoscopic Ruler for Super-Resolution Microscopy, Angewandte Chemie Int. Ed.
48, 8870-8873(2009).

F. C. Simmel, Processive motion of bipedal DNA walkers, ChemPhysChem 10,
2593-2597 (2009).

S. Kaniber, F. C. Simmel, A. W. Holleitner, I. Carmeli, The optoelectronic properties of a photosystem I - carbon nanotube hybrid system, Nanotechnology 20, art. 345701 (2009).

2008

R. Jungmann, T. Liedl, T. L. Sobey, W. Shih, and F. C. Simmel, Isothermal assembly of DNA origami structures using denaturing agents, Journal of the American Chemical Society,  130, 10062-10063 (2008). http://dx.doi.org/10.1021/ja8030196

F. C. Simmel, Three-dimensional nanoconstruction with DNA, Angewandte Chemie Int. Ed. 47, 5884-5887  (2008).

R. Jungmann, S. Renner,  F. C. Simmel, From DNA nanotechnology to synthetic biology, HFSP Journal 2, 99-109 (2008).

M. Olapinski, S. Manus, N. Fertig, F. C. Simmel, Probing whole cell currents in high-frequency fields: Identification of thermal effects, Biosensors and Bioelectronics 23, 872-878  (2008).