Publications

2020

Bookchapter

We share some methods and protocols for the generation of DNA-based membrane pores in a bookchapter:

K. Göpfrich, A. Ohmann & U. F. Keyser. Design and Assembly of Membrane-Spanning DNA Nanopores. In: Nanopore Technology (Ed. M. Fahie), 2020. ISBN 978-1-0716-0806-7

Advanced Intelligent Systems

We found that actin-containing droplet show directional motion due to the Marangoni effect:

B. Haller, K. Jahnke, M. Weiss, K. Göpfrich, I. Platzman* & J. P. Spatz*. Autonomous Directional Motion of Actin-Containing Cell-Sized Droplets, Advanced Intelligent Systems,  2020. In press.

IFN-gamma

We contributed to an assay to evaluate cell cytotoxicity and cytokine release on a single-cell level:

S. Antona, T. Abele, K. Jahnke, Y. Dreher, K. Göpfrich, I. Platzman & J. P. Spatz. Droplet‐Based Combinatorial Assay for Cell Cytotoxicity and Cytokine Release Evaluation, Advanced Functional Materials, 2003479, 2020. https://doi.org/10.1002/adfm.202003479

Polymersomes

Cholesterol-tagged DNA does not only self-assemble into lipid membranes but also polymersomes – under the right conditions:

R. Luo, K. Göpfrich, I. Platzman & J. P. Spatz. DNA-Based Assembly of Multi-Compartment Polymersome Networks, Advanced Functional Materials, 2003480, 2020. https://doi.org/10.1002/adfm.202003480

AdvBiosys-2020

We interface DNA nanotechnology and actin networks and show that light-triggered contaction breaks the symmetry:

K. Jahnke, M. Weiss, C. Weber, I. Platzman*, K. Göpfrich* & J. P. Spatz*. Engineering Light‐Responsive Contractile Actomyosin Networks with DNA Nanotechnology, Advanced Biosystems 2020. https://doi.org/10.1002/adbi.202000102

ACS Omega 2020

We used DNA functionalization and electrocoalescence to filter the content of microfluidic droplets:

C. Frey, K. Göpfrich, S. Pashapour, I. Platzman & J. P. Spatz. Electrocoalescence of Water-in-Oil Droplets with a Continuous Aqueous Phase: Implementation of Controlled Content Release. ACS Omega 2020. https://doi.org/10.1021/acsomega.0c00344

We reconfigure plasmonic DNA origami in microfluidic droplets:

K. Göpfrich*, M. J. Urban, C. Frey, I. Platzman, J. P. Spatz* & N. Liu*. Dynamic Actuation of DNA-Assembled Plasmonic Nanostructures in Microfluidic Cell-Sized Compartments. Nano Letters 20, 1571-1577, 2020https://doi.org/10.1007/978-981-13-9791-2_11

2019

Bookcover Springer

We contributed a bookchapter on DNA nanopores:

K. Göpfrich & U. F. Keyser. DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. In: Biological and Bio-inspired Nanomaterials, 2019https://doi.org/10.1007/978-981-13-9791-2_11

Our view on synthetic biology published in Heidelberg University’s research magazine Ruperta Carola (mostly in German):

K. Göpfrich, I. Platzman & J. P. Spatz. Aus dem Baukasten der molekularen Ingenieure. Auf dem Weg zur synthetischen Zelle, Ruperto Carola, 106-113 2019. [PDF]

Shielding cholesterol-tags with ssDNA

We show that single-stranded DNA overhangs can wrap around a cholesterol-tag and thereby prevent aggregation of cholesterol-modified DNA nanostructures:

A. Ohmann, K. Göpfrich, H. Joshi, R. F. Thompson, D. Sobota, N. A. Ranson, A. Aksimentiev & U. F. Keyser. Controlling aggregation of cholesterol-modified DNA nanostructures. Nucleic Acids Research 47, 11441–11451, 2019https://doi.org/10.1093/nar/gkz914

Making GUVs by shaking

We establish a method for the formation of giant unilamellar vesicles for the assembly of synthetic cells, offering straight-forward encapsulation of content:

K. Göpfrich, B. Haller, O. Staufer, Y. Dreher, U. Mersdorf, I. Platzman & J. P. Spatz, One-Pot Assembly of Complex Giant Unilamellar Vesicle-Based Synthetic Cells. ACS Synthetic Biology, 2019. https://doi.org/10.1021/acssynbio.9b00034

Video protocol illustrating the method: https://youtu.be/vOPp97toPAw

Functionalization of microfluidic droplets

We demonstrate a universal strategy for the functionalization of microfluidic droplets by attaching reactive groups and components to cholesterol-tagged DNA handles:

K. Jahnke, M. Weiss, C.  Frey, S. Antona, J.-W. Janiesch, I. Platzman, K. Göpfrich* & J. P. Spatz*, Programmable Functionalization of Surfactant-Stabilized Microfluidic Droplets via DNA-Tags. Advanced Functional Materials, 2019. https://doi.org/10.1002/adfm.201808647

2018

Droplet-stabilized GUVs

By tailoring the charge density at the interface of microfluidic droplets, we control the transition between multicompartment systems and GUVs:

B. Haller, K. Göpfrich, M. Schröter, J.-W. Janiesch, I. Platzman & J. P. Spatz, Charge-controlled microfluidic formation of lipid-based single- and multicompartment systems. Lab on a Chip, 2018. https://doi.org/10.1039/C8LC00582F

Journal cover

In this review, we discuss how microfluidics and DNA nanotechnology can be used as tools to assemble complex synthetic cells.

K. Göpfrich*, I. Platzman* & J. P. Spatz*, Mastering Complexity: Towards Bottom-up Construction of Multifunctional Eukaryotic Synthetic Cells. Trends in Biotechnology, 2018. https://doi.org/10.1016/j.tibtech.2018.03.008

Watch a short video about our review here.

MD simulation of the DNA-based scramblase

We demonstrate that membrane-spanning DNA nanopores are not just mimics of ion channels: They can also transport flip lipids from one bilayerleaflet to the other, like natural scramblases.

A. Ohmann, C.-Y. Li, C. Maffeo, K. Al Nahas, K. N. Baumann, K. Göpfrich, J. Yoo, U. F. Keyser, A. Aksimentiev, Outperforming nature: synthetic enzyme built from DNA flips lipids of biological membranes at record rates. Nature Communications, 2018https://doi.org/10.1038/s41467-018-04821-5

In the news in c&en.

2017

DNA-based membrane pores

Kerstin’s PhD thesis in the group of Prof. Ulrich F. Keyser at the University of Cambridge, on the assembly synthetic membrane pores from DNA.

K. Göpfrich, Rational Design of DNA-Based Lipid Membrane Pores. PhD Thesis, 2017https://doi.org/10.17863/CAM.15517

Thanks to Gates Cambridge, the Winton Programme for the Physics of Sustainability and the Oppenheimer Trust for their generous support.

2016

DNA origami porin

We built the largest man-made pore in lipid membranes to date and determine its conductance properties with single-molecule experiments and molecular dynamics simulations:

K. Göpfrich, C.-Y. Li, M. Ricci, S. P. Bhamidimarri, J. Yoo, B. Gyenes, A. Ohmann, M. Winterhalter, A. Aksimentiev & U. F. Keyser, Large-Conductance Transmembrane Porin Made from DNA Origami, ACS Nano, 2016. http://pubs.acs.org/doi/abs/10.1021/acsnano.6b03759

Ion conduction pathways across membranes can be lined by the lipids themselves. We demonstrated the formation of stable DNA-lipid pores induced by a single transmembrane-spanning DNA duplex:

K. Göpfrich, C.-Y. Li, C.-Y., I. Mames, S. P. Bhamidimarri, M. Ricci, J. Yoo, A. Mames, A. Ohmann, M. Winterhalter, E. Stulz, A. Aksimentiev & U. F. Keyser, Ion channels made from a single membrane-spanning DNA duplex. Nano Letters, 2016. http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.6b02039

DNA tiles

We study transitions from bound to unbound cluster growth using computational models and DNA-tile self-assembly experiments:

S. Tesoro, K. Göpfrich, T. Kartanas, U. F. Keyser & S. E. Ahnert. Non-deterministic self-assembly with asymmetric interactions can lead to tunable self-limiting cluster growth. Physical Review E, 2016. http://journals.aps.org/pre/abstract/10.1103/PhysRevE.94.022404

2015

DNA-based ion channel

We created the smallest membrane-inserting DNA nanostructure to date, approaching the dimensions of natural ion channels:

K. Göpfrich, T. Zettl, A. E. C. Meijering, S. Hernández-Ainsa, S. Kocabey, T. Liedl & U. F. Keyser, DNA-tile structures lead to ionic currents through lipid membranes. Nano Letters, 2015. http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b00189

2014

Journal cover

DNA-based membrane pores exhibit voltage-dependent conductance states, reminiscent of gating observed for natural membrane pores:

A. Seifert*, K. Göpfrich*, J. R. Burns, N. Fertig, U. F. Keyser & S. Howorka, Bilayer-spanning DNA nanopores with voltage-switching between open and closed state. ACS Nano, 2014 (*equal contribution). http://pubs.acs.org/doi/abs/10.1021/nn5039433

2013

Journal cover

Two porphyrin-tags anchor a simple DNA nanopore in the lipid membrane and serves as fluorescent dyes at the same time:

J. R. Burns, K. Göpfrich, J. W. Wood, V. V. Thacker, E. Stulz, U. F. Keyser & S. Howorka, Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor. Angewandte Chemie International Edition, 2013. http://onlinelibrary.wiley.com/doi/10.1002/anie.201305765/abstract

DNA nanopore

We modify solid-state nanopores with DNA origami to control their pore size and the positioning of binding sites for specific analytes:

S. Hernández-Ainsa, N. A. W. Bell, V. V.  Thacker, K. Göpfrich, K. Misiunas, M. E. Fuentes-Perez, F. Moreno-Herrero & U. F. Keyser, DNA origami nanopores for controlling DNA translocation. ACS Nano, 2013. http://pubs.acs.org/doi/abs/10.1021/nn401759r

alpha-hemolysin

The frequency of DNA translocation through the protein nanopore alpha-hemolysin is significantly enhanced at pH 6 compared to pH 8:

K. Göpfrich, C. V. Kulkarni, O. J. Pambos & U. F. Keyser, Lipid nanobilayers to host biological nanopores for DNA translocations. Langmuir, 2013. http://pubs.acs.org/doi/abs/10.1021/la3041506