SFB 1032: Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions
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Publications Area A

A01

"Strep-Tag II and Monovalent Strep-Tactin as Novel Handles in Single-Molecule Cut-and-Paste"
Authors: Katherine R. Erlich, Fabian Baumann, Diana A. Pippig and H. E. Gaub.
small methods, DOI: 10.1002/smtd.201700169, First published: 18 July 2017

"C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA"
Authors: Daniela Aschenbrenner, Fabian Baumann, Lukas F. Milles, Dr. Diana A. Pippig and H. E. Gaub.
ChemPhysChem, DOI: 10.1002/cphc.201500193, Vol. 16, Issue 10, pg 2085–2090, July 20, 2015

"Tip localization of an atomic force microscope in transmission microscopy with nanoscale precision"
Authors: Fabian Baumann, Stephan F. Heucke, Diana A. Pippig and H. E. Gaub.
Review Sci. Instruments, 86, 035109 (2015); doi.org/10.1063/1.4915145, 20th March 2015

"Parallel Force Assay for Protein-Protein Interactions"
Authors: Daniela Aschenbrenner, Diana A. Pippig, Kamila Klamecka, Katja Limmer, Heinrich Leonhardt and H. E. Gaub.
PLOS, DOI: 10.1371/journal.pone.0115049, Published: December 29, 2014

"A Force-Based, Parallel Assay for the Quantification of Protein-DNA Interactions"

Authors: K. Limmer, D. A. Pippig, D. Aschenbrenner and H. E. Gaub.
PLOS one, DOI: 10.1371/journal.pone.0089626, February 2014

A02

"A self-assembled nanoscale robotic arm controlled by electric fields"
Authors: Enzo Kopperger, Jonathan List, Sushi Madhira, Florian Rothfischer,Don C. Lamb (B03) and Friedrich C. Simmel.
Science 359 (6373), 296-301. DOI: 10.1126/science.aao4284, 19 January 2018

"Long-range movement of large mechanically interlocked DNA nanostructures"
Authors: Jonathan List, Elisabeth Falgenhauer, Enzo Kopperger, Günther Pardatscher & Friedrich C. Simmel.
Nature Communications 7, Article number:12414, doi:10.1038/ncomms12414, August 5, 2016

"Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases"
Authors: Sandra Sagredo, Tobias Pirzer, Ali Aghebat Rafat, Marisa A. Goetzfried, Gabriel Moncalian,
Friedrich C. Simmel and Fernando de la Cruz.
Angewandte Chemie Int. Ed Engl., 55(13):4348-52. doi: 10.1002/anie.201510313, Mar 18, 2016

"A Compact DNA Cube with Side Length 10 nm"
Authors: Max B. Scheible, Luvena L. Ong, Johannes B. Woehrstein, Ralf Jungmann, Peng Yin and F. C. Simmel.
Small Journal,Volume 11, Issue 39, pages 5200–5205, DOI: 10.1002/smll.201501370, October 21, 2015

"Diffusive Transport of Molecular Cargo Tethered to a DNA Origami Platform"
Authors: Enzo Kopperger , Tobias Pirzer and F. C. Simmel.
Nano Lett., 2015, 15 (4), pp 2693–2699, DOI: 10.1021/acs.nanolett.5b00351, March 5, 2015

"Membrane-Assisted Growth of DNA Origami Nanostructure Arrays"
Authors: Samet Kocabey, Susanne Kempter, Jonathan List, Yongzheng Xing, Wooli Bae, Daniel Schiffels,
William M. Shih, F. C. Simmel and Tim Liedl (A06)
ACS Nano, 2015, 9 (4), pp 3530–3539, DOI: 10.1021/acsnano.5b00161, March 3, 2015

"Robustness of Localized DNA Strand Displacement Cascades"
Authors: M. Teichmann, E. Kopperger and F. C. Simmel.
ACS Nano, 8, 8487-8496, 10.1021/nn503073p, August 2014

"DNA Nanostructures Interacting with Lipid Bilayer Membranes"
Authors: M. Langecker, V. Arnaut, J. List and F. C. Simmel.
Acc. Chem. Res., dx.doi.org/10.1021/ar500051r, 47, 1807−1815, May 2014

"Hydrophobic Actuation of a DNA Origami Bilayer Structure"
Authors: J. List, M. Weber and F. C. Simmel.
Angew. Chemie, DOI: 10.1002/anie.201310259, Ed. 2014, 53, 4236 –4239, March 11, 2014

"Single Molecule Characterization of DNA Binding and Strand Displacement Reactions on Lithographic DNA Origami Microarrays"
Authors: M. B. Scheible, G. Pardatscher, A. Kuzyk and F. C. Simmel.
Nano Lett., dx.doi.org/10.1021/nl500092j, 14, 1627−1633, February 2014

A03

"Optimal Compartmentalization Strategies for Metabolic Microcompartments."
Authors: Florian Hinzpeter, Ulrich Gerland and Filipe Tostevin
Biophysical Journal, Volume 112, Issue 4 February 28, 2017

Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information
Authors: Patrick Hillenbrand, Ulrich Gerland und Gasper Tkačik.
PLOS ONE, DOI:10.1371/journal.pone.0163628, September 27, 2016

"A microfluidics approach to study the accumulation of molecules at basal lamina interfaces"
Authors: Fabienna Arends, Sabine Sellner, Philipp Seifert, Ulrich Gerland, Markus Rehberg (B10) and Oliver Lieleg (B7).
Lab Chip,15, 3326-3334, DOI: 10.1039/C5LC00561B, 02 Jul 2015

"Clustering and Optimal Arrangement of Enzymes in Reaction-Diffusion Systems."
Authors: Alexander Buchner, Filipe Tostevin and Ulrich Gerland.
Physical Review Letters, May 17, 2013, DOI:10.1103/110.208104

"Toward a unified physical model of nucleosome patterns flanking transcription start sites"
Authors: Wolfram Möbius, Brendan Osberg, Alexander M. Tsankov, Oliver J. Rando and Ulrich Gerland.
PNAS, 201214048, March 18, 2013

A04

"Proton gradients and pH oscillations emerge from heat flow at the microscale."
Authors: Lorenz M. R. Keil, Friederike M. Möller, Michael Kieß, Patrick W. Kudella and Christof B. Mast
Nature Communications 8, Article number: 1897 (2017)doi:10.1038/s41467-017-02065-3, December 01, 2017

"Reversible Switching of Cooperating Replicators."
Authors: Georg C. Urtel, Thomas Rind and Dieter Braun.
Phys. Rev. Lett. 118, 078102, Published 15 February, 2017

"Emergence of Life from Trapped Nucleotides? Non-Equilibrium ­Behavior of Oligonucleotides in Thermal Gradients."
Authors: Emil Dandanell Agerschoua, Christof B. Mast and Dieter Braun.
Synlett; 28(01): 56-63, DOI: 10.1055/s-0036-1588653, 2017

"Heat-Flow-Driven Oligonucleotide Gelation Separates Single-Base Differences."
Authors: Matthias Morasch, Dieter Braun und Christof B. Mast.
Angew. Chemie, DOI: 10.1002/anie.201601886, Volume 55, Issue 23, Pages 6676–6679, June 1, 2016

"Photochemical Microscale Electrophoresis Allows Fast Quantification of Biomolecule Binding"
Authors: Friederike M. Möller, Michael Kieß and Dieter Braun.
J. Am. Chem. Soc., 2016, 138 (16), pp 5363–5370, DOI: 10.1021/jacs.6b01756, April 4, 2016

"Single molecule imaging in living Drosophila embryos with reflected light-sheet microscopy"
Authors: Greiss F., Deligiannaki M., Jung C., Gaul U. and Dieter Braun.
Biophys J.;110(4):939-46. doi: 10.1016/j.bpj.2015.12.035, 2016 Feb 23

"Quantitative thermophoretic study of disease-related protein aggregates"
Authors: Manuel Wolff , Judith J. Mittag, Therese W. Herling, Erwin De Genst, Christopher M. Dobson, Tuomas P. J. Knowles, Dieter Braun and Alexander K. Buell.
Nature, doi:10.1038/srep22829, Scientific Reports 6, Article number: 22829, Feb. 2016

"Understanding the similarity in thermophoresis between single- and double-stranded DNA or RNA"
Authors: Maren Reichl, Mario Herzog, Ferdinand Greiss, Manuel Wolff and Dieter Braun.
Phys. Rev. E 91, 062709, Vol. 91, Iss. 6,  – Published 11 June 2015

"Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length"
Authors: Moritz Kreysing, Lorenz Keil, Simon Lanzmich and Dieter Braun.
Nature Chemistry, Vol. 7, pages 203–208, DOI:10.1038/nchem.2155, 26 January 2015

Thermophoretic Manipulation of Molecules inside Living Cells

Authors: Maren R. Reichl and Dieter Braun.
J. Am. Chem. Soc., 2014, 136 (45), pp 15955–15960, DOI: 10.1021/ja506169b
Publication Date (Web): August 29, 2014

"Thermophorese in Nanoliter-Tropfen zur Quantifizierung von Aptamer-Bindungen"
Authors: S. I. Seidel, N. Markwardt, S. Lanzmich and Dieter Braun.
Angew. Chemie, Volume 126, Issue 30, pages 8082–8086, DOI: 10.1002/ange.201402514, July 21, 2014

A05

"Dendrimer‐Based Signal Amplification of Click‐Labelled DNA in Situ."
Authors: N.,  Raddaoui, S. Stazzoni, Dr. L. Möckl, B. Viverge, F. Geiger, H. Engelke (B11), C. Bräuchle and Th. Carell.
CHEM BIOCHEM, DOI: 10.1002/cbic.201700209, 22. June 2017

"Genetically designed biomolecular capping system for mesoporous silica nanoparticles enables receptor-mediated cell uptake and controlled drug release"
Authors: Stefan Datz, Christian Argyo, Michael Johannes Gattner, Veronika Weiss, Korbinian Brunner, Johanna Bretzler, Constantin von Schirnding, Adriano A. Torrano, Fabio Spada, Milan Vrabel, Hanna Engelke, C Brauchle, Thomas Carell and Thomas Bein.
Nanoscale, DOI: 10.1039/C5NR08163G, 17 Feb 2016

"Cell-Penetrating and Neurotargeting Dendritic siRNA Nanostructures"
Authors: Korbinian Brunner, Johannes Harder, Tobias Halbach, Julian Willibald, Fabio Spada, Felix Gnerlich, Konstantin Sparrer, Andreas Beil, Leonhard Möckl, Christoph Bräuchle, Karl-Klaus Conzelmann and T. Carell.
Angewandte Chemie I. E., Vol. 54, Issue 6, pages 1946–1949, DOI: 10.1002/anie.201409803, February 2, 2015

“Post-It” Type Connected DNA Created with a Reversible Covalent Cross-Link

Autors: María Tomás-Gamasa, Sascha Serdjukow, Meng Su, Markus Müller and T. Carell.
Angewandte Chemie I.E., Vol. 54, Issue 3, pages 796–800, DOI: 10.1002/anie.201407854, January 12, 2015

"DNA based multi-copper ions assembly using combined pyrazole and salen ligandosides"
Authors: Meng Su,  María Tomás-Gamasa and T. Carell.
Chemical Science, DOI: 10.1039/c4sc01567c, 5th August 2014

"Synthesis and properties of a Cu(II) complexing pyrazole ligandoside in DNA"
Authors: M. Su, Maria Tomás-Gamasa, S. Serdjukow, P. Mayer and T. Carell.
Chem. Commun., 50, 409, 2014, DOI: 10.1039/c3cc47561a

"Synthesis of c-labeled nucleoside 50-triphosphates using click chemistry"
Authors: S. Serdjukow, F. Kink, B. Steigenberger, M. Toma´s-Gamasa and T. Carell.
Chem. Commun., 50, 1861, 2014, DOI: 10.1039/c3cc48937j

"Synthesis of e-N-propionyl-, e-N-butyryl-, and e-N-crotonyl-lysine containing histone H3 using the pyrrolysine system"
Authors: Michael J. Gattner, Milan Vrabel and T. Carell.
Chem. Commun., 49, 379,2013, DOI: 10.1039/c2cc37836a

A06

"Molecular force spectroscopy with a DNA origami–based nanoscopic force clamp"
Authors: Philipp C. Nickels, Bettina Wünsch, Phil Holzmeister, Wooli Bae, Luisa M. Kneer, Dina Grohmann, Philip Tinnefeld and Tim Liedl.
Science, Vol. 354, Issue 6310, pp. 305-307, DOI: 10.1126/science.aah5974, 21 Oct 2016

"DNA Origami Seesaws as Comparative Binding Assay"
Authors: Philipp C. Nickels, H. C. Høiberg, Stephanie S. Simmel, Phil Holzmeister, Philip Tinnefeld and Tim Liedl
CHEMBIOCHEM, DOI: 10.1002/cbic.201600059, May 6, 2016

"Membrane-Assisted Growth of DNA Origami Nanostructure Arrays"

Authors: Samet Kocabey, Susanne Kempter, Jonathan List, Yongzheng Xing, Wooli Bae, Daniel Schiffels,
William M. Shih, F. C. Simmel (A02) and Tim Liedl.
ACS Nano, 2015, 9 (4), pp 3530–3539, DOI: 10.1021/acsnano.5b00161, March 3, 2015

"DNA nanotubes as intracellular delivery vehicles in vivo"
Authors: Sabine Sellner, Samet Kocabey, Katharina Nekolla, Fritz Krombach, Tim Liedl and Markus Rehberg (B10).
Biomaterials, Volume 53, Pages 453–463, doi:10.1016/j.biomaterials.2015.02.099, Published: June, 2015

"Plasmonic DNA-Origami Nanoantennas for Surface-Enhanced Raman Spectroscopy"
Authors: P. Kühler, R. Schreiber, E.-M. Roller, T. Liedl, T. Lohmüller (A08), J. Feldmann
Nano Lett., 2014, 14 (5), pp 2914–2919, DOI: 10.1021/nl5009635, April 23, 2014

"Nucleic acid nanostructures for biomedical applications"
Authors: David Smith, Verena Schüller, Christian Engst, Joachim Rädler (B01) and Tim Liedl.
Future Medicine, London, January 2013, Vol. 8, No. 1, Pages 105-121 , DOI 10.2217

A07

"Transferable Organic Semiconductor Nanosheets for Application in Electronic Devices"
Authors: Simon Noever, Michael Eder, Fabio del Giudice, Jan Martin, Franz X. Werkmeister, Stefan Hallwig,
Stefan Fischer, Oliver Seeck, Nils-Eike weber, Clemens Liewald, Fritz Keilmann, Andrey Turchanin and Bert A. Nickel.
Advanced Materials, DOI: 10.1002/adma.201606283, 8 May 2017

"Fast detection of blood gases by solution gated organic field effect transistors"
Authors: Franz X. Werkmeister and Bert A. Nickel.
ELSEVIER, Organic Electronics, doi.org/10.1016/j.orgel.2016.09.025, Vol. 39, Pag. 113–117, December 2016

"Influence of Ibuprofen on Phospholipid Membranes"
Authors: Sebastian Jaksch, Frederik Lipfert, Alexandros Koutsioubas, Stefan Mattauch, Olaf Holderer, Oxana Ivanova, Henrich Frielinghaus, Samira Hertrich, Stefan F. Fischer and Bert Nickel.
Phys. Rev. E 91, 022716, DOI: 10.1103/PhysRevE.91.022716, 2015

"Cell Motility on Polyethylene Glycol Block Copolymers Correlates to Fibronectin Surface Adsorption"

Authors: Peter J. F. Röttgermann, Samira Hertrich, Ida Berts, Max Albert, Felix J. Segerer, Jean-François Moulin,
Bert Nickel and Joachim Rädler (B01).
Macromolecular Bioscience, Vol. 14, Issue 12, pages 1755–1763, DOI: 10.1002/mabi.201400246, Dec. 2014

"Towards flexible organic thin film transistors (OTFTs) for biosensing"
Authors: Franz Werkmeister and Bert Nickel.
Journal of Materials Chemistry B, May 2013, DOI: 10.1039/c3tb20590h

A08

Targeting de novo lipogenesis as a novel approach in anti-cancer therapy
Authors: K. Stoiber, O. Nagło, C. Pernpeintner, S. Zhang, A. Koeberle, M. Ulrich, O. Werz, R. Mueller, S. Zahler (B08), T. Lohmüller, J. Feldmann and S. Braig
British Journal of Cancer 118 (1), 43-51 (2018)

Optofluidic transport and manipulation of plasmonic nanoparticles by thermocapillary convection
Authors: F. Winterer, C. Maier, C. Pernpeinter and T. Lohmüller
Soft Matter, 14, 628-634 (2018)

Light-Controlled Membrane Mechanics and Shape Transitions of Photoswitchable Lipid Vesicles
Authors: C. Pernpeintner, J. A. Frank, P. Urban, C. R. Roeske, S. D. Pritzl, D. Trauner (B09) and T. Lohmüller
Langmuir 33 (16), 4083–4089 (2017)

Controlling non-equilibrium structure formation on the nanoscale
Authors: B. Buchmann, F. Maned Hecht, C. Pernpeintner, T. Lohmüller and A. Bausch (A10)
ChemPhysChem 18 (23), 3437–3442 (2017)

Detecting swelling states of red blood cells by “Cell–Fluid Coupling Spectroscopy
Authors: C. Zensen, I. E. Fernandez, O. Eickelberg, J. Feldmann and T. Lohmüller
Advanced Science 4 (2), 1600238 (2017)

“Bending Gold Nanorods with Light”
Authors: A. Babynina, M. Fedoruk, P. Kühler, A. Meledin, M. Döblinger and T. Lohmueller
Nano Letters 16 (10), 6485-6490 (2016)

“Quantitative single molecule surface-enhanced Raman scattering by optothermal tuning of DNA origami assembled plasmonic nanoantennas”
Authors: S. Simoncelli, E-M. Roller, P. Urban, R. Schreiber, A. J. Turberfield, T. Liedl (A06), and T. Lohmüller
ACS Nano 10 (11), 9809-9815 (2016)

"Reversible control of current across lipid membranes by local heating"
Authors: P. Urban, S.R. Kirchner, C. Mühlbauer, T. Lohmüller and J. Feldmann.
Scientific reports 6, 22686, March 2016

"Pushing nanoparticles with light- a femnewton resolved measurement of optical scattering forces"
Authors: C. Zensen, N. Villadsen, F. Winterer, S.R. Keiding and T. Lohmüller.
APL Photonics, March 2016

"Optical Injection of Gold Nanoparticles into Living Cells."
Authors: M.Li, T. Lohmüller, and J. Feldmann.
Nano Letters 15 (1), 770-775, December 11, 2015

“Analyzing the Movement of the Nauplius 'Artemia Salina' by Optical Tracking of Plasmonic Nanoparticles”
Authors: S. R. Kirchner, M. Fedoruk, T. Lohmüller and J. Feldmann.
J Vis Exp 2014 15(89), Epub 15 Jul 2014

"Direct optical monitoring of flow generated by bacterial flagellar rotation"
Authors: S. R. Kirchner, S. Nedev, S. Carretero-Palacios, A. Mader, M. Opitz, T. Lohmüller and J. Feldmann
Appl. Phys. Lett. 104, 093701 (2014)

Plasmonic Nanoantenna Arrays for Surface-Enhanced Raman Spectroscopy of Lipid Molecules Embedded in a Bilayer Membrane"
Autors: P. Kühler, M. Weber and T. Lohmüller.
ACS Appl. Mater. Interfaces, 2014, 6 (12), pp 8947–8952, DOI: 10.1021/am5023418, June 4, 2014

"Plasmonic DNA-Origami Nanoantennas for Surface-Enhanced Raman Spectroscopy"
Authors: P. Kühler, R. Schreiber, E.-M. Roller, T. Liedl (A06), T. Lohmüller, J. Feldmann
Nano Lett., 2014, 14 (5), pp 2914–2919, DOI: 10.1021/nl5009635, April 23, 2014

"Optical trapping and manipulation of plasmonic nanoparticles: fundamentals, applications, and perspectives"

Authors: A. S. Urban, S. Carretero-Palacios, A. A. Lutich, T. Lohmüller, J. Feldmann and Frank Jäckel
Nanoscale, 2014,6, 4458-4474, DOI: 10.1039/C3NR06617G, 24 Mar 2014

“Nanolithography by Plasmonic Heating and Optical Manipulation of Gold Nanoparticles”
Authors: M. Fedoruk, M. Meixner, S. Carretero-Palacios, T. Lohmüller and J. Feldmann
ACS Nano, 2013, 7 (9), pp 7648–7653, DOI: 10.1021/nn402124p, August 13, 2013

"Synthesis of Gold Nanostar Arrays as Reliable, Large-Scale, Homogeneous Substrates for Surface-Enhanced Raman Scattering Imaging and Spectroscopy"

Authors: L. Osinkina, T. Lohmüller, F. Jäckel, and J. Feldmann
The Journal of Physical Chemistry C, March 4, 2013; DOI: 10.1021/jp312149d

"Shrink-to-fit Plasmonic Nanostructures"
Authors: A. S. Urban, M. Fedoruk, S. Nedev, A. Lutich, T. Lohmüller and J. Feldmann.
Advanced Optical Materials, 1, Feb 06 2013,123-217, DOI: 10.1002/adom.201200031

A09

"MinE conformational switching confers robustness on self-organized Min protein patterns"
Authors: Jonas Denk, Simon Kretschmer, Jacob Halatek, Caroline Hartl, Petra Schwille and Erwin Frey (B02).
PNAS, 201719801; doi.org/10.1073/pnas.1719801115, April 16, 2018.

"Surface topology assisted alignment of Min protein waves"
Authors: Katja Zieske, Jakob Schweizer and Petra Schwille.
FEBSLetters, Volume 588, Issue 15, Pages 2545–2549, doi:10.1016/j.febslet.2014.06.026, August 2014

"Reconstitution of Pole-to-Pole Oscillations of Min Proteins in Microengineered Polydimethylsiloxane Compartments."
Authors: Katja Zieske and Petra Schwille.
Angewandte Chemie Int. Ed., January 2013, 52: 459–462, DOI: 10.1002/anie.201207078

A11

"Sub–100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA"
Authors: Johannes B. Woehrstein, Maximilian T. Strauss, Luvena L. Ong, Bryan Wei, David Y. Zhang, Ralf Jungmann and Peng Yin.
Science Advances, Vol. 3, no. 6, e1602128, DOI: 10.1126/sciadv.1602128, 21 Jun 2017