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

A01

"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. Pippig1 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

"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

"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

"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

"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

"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

"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