Publications

2021

How can you build up structures on the inside of synthetic cells? With two-photon 3D laser printing:

T. Abele, T. Messer, K. Jahnke, M. Hippler, M. Bastmeyer, M. Wegener & K. Göpfrich. Two-photon 3D laser printing inside synthetic cells, Advanced Materials (2021). DOI: 10.1002/adma.202106709

We divide DNA-containing giant unilamellar lipid vesicles with light-triggered lipid peroxidation:

Y. Dreher, K. Jahnke, M. Schröter & K. Göpfrich. Light-Triggered Cargo Loading and Division of DNA-Containing Giant Unilamellar Lipid Vesicles, Nano Letters (2021). DOI: 10.1021/acs.nanolett.1c00822

We use top-down engineered E. coli as actuators in bottom-up assembled synthetic cells:

K. Jahnke, N. Ritzmann, J. Fichtler, A. Nitschke, Y. Dreher, T. Abele, G. Hofhaus, I. Platzman, R. Schröder, D. Müller, J. Spatz & K. Göpfrich. Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells, Nature Communications 12, 3967, 2021. https://doi.org/10.1038/s41467-021-24103-x

Press release: https://www.mr.mpg.de/14524114/synthetic-biology-bottom-up-meets-top-down

Behind the Paper: https://bioengineeringcommunity.nature.com/posts/synthetic-biology-bottom-up-meets-top-down

We show with experiments and molecular dynamics simulations that the choice of fluorophores matters for dynamic DNA nanostructures:

K. Jahnke, H. Grubmüller,  M. Igaev & K. Göpfrich. Choice of fluorophore affects dynamic DNA nanostructures, Nucleic Acids Research gkab201, 2021 https://doi.org/10.1093/nar/gkab201  

We provide tips, tricks and tools for the functionalization of cellular membranes with DNA nanotechnology  and review recent applications:

A. Schönit, A. Cavalcanti-Adam & K. Göpfrich. Functionalization of Cellular Membranes with DNA Nanotechnology, Trends in Biotechnology, 2021. https://doi.org/10.1016/j.tibtech.2021.02.002

2020

Angewandte Chemie

We divide phase-separated GUVs with enzymatic reactions or locally with light and describe the process with an analytical model:

Y. Dreher, K. Jahnke, E. Bobkova, J.P. Spatz & K. Göpfrich. Division and regrowth of phase‐separated giant unilamellar vesicles, Angewandte Chemie, 2020. https://doi.org/10.1002/ange.202014174

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

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. https://doi.org/10.1002/aisy.202000190

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

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