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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering The Pennsylvania State University University Park PA 16802 USA
| | - Yong Wang
- Department of Biomedical Engineering The Pennsylvania State University University Park PA 16802 USA
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2
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Shi P, Wang Y. Synthetic DNA for Cell-Surface Engineering. Angew Chem Int Ed Engl 2021; 60:11580-11591. [PMID: 33006229 DOI: 10.1002/anie.202010278] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 12/14/2022]
Abstract
The cell membrane is not only a physical barrier, but also a functional organelle that regulates the communication between a cell and its environment. The ability to functionalize the cell membrane with synthetic molecules or nanostructures would advance cellular functions beyond what evolution has provided. The aim of this Minireview is to introduce recent progress in using synthetic DNA and DNA-based nanostructures for cell-surface engineering. We first introduce chemical conjugation and physical binding methods for monovalent and polyvalent surface engineering. We then introduce the application of these methods for either the promotion or inhibition of cell-environment communication in numerous applications, including the promotion of cell-cell recognition, regulation of intracellular pathways, protection of therapeutic cells, and sensing of the intracellular and extracellular microenvironments. Lastly, we summarize current challenges existing in this area and potential solutions to solve these challenges.
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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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3
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Hu Y, Domínguez CM, Christ S, Niemeyer CM. Postsynthetic Functionalization of DNA-Nanocomposites with Proteins Yields Bioinstructive Matrices for Cell Culture Applications. Angew Chem Int Ed Engl 2020; 59:19016-19020. [PMID: 32681679 PMCID: PMC7589387 DOI: 10.1002/anie.202008471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/13/2020] [Indexed: 11/08/2022]
Abstract
We report on the directed postsynthetic functionalization of soft DNA nanocomposite materials with proteins. Using the example of the functionalization of silica nanoparticle-modified DNA polymer materials with agonists or antagonists of the epidermal growth factor receptor EGFR cell membrane receptor, we demonstrate that hierarchically structured interfaces to living cells can be established. Owing to the modular design principle, even complex DNA nanostructures can be integrated into the materials, thereby enabling the high-precision arrangement of ligands on the lower nanometer length scale. We believe that such complex biohybrid material systems can be used for new applications in biotechnology.
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Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Carmen M. Domínguez
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Sophina Christ
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
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4
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Hu Y, Domínguez CM, Christ S, Niemeyer CM. Postsynthetic Functionalization of DNA‐Nanocomposites with Proteins Yields Bioinstructive Matrices for Cell Culture Applications. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Carmen M. Domínguez
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Sophina Christ
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT) Institute for Biological Interfaces (IBG 1) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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5
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Burgahn T, Garrecht R, Rabe KS, Niemeyer CM. Solid-Phase Synthesis and Purification of Protein-DNA Origami Nanostructures. Chemistry 2019; 25:3483-3488. [PMID: 30609150 DOI: 10.1002/chem.201805506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Indexed: 12/13/2022]
Abstract
We present a facile method for the combined synthesis and purification of protein-decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the "halo-based oligonucleotide binder" (HOB), a variant of Halo-tag, the "SpyTag/SpyCatcher" (ST/SC) system, and the enzymatic "ybbR tag" coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface-based cell assays.
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Affiliation(s)
- Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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6
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Dubel N, Liese S, Scherz F, Seitz O. Untersuchungen zu Grenzen der Bivalenz mit DNA-basierter räumlicher Rasterung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Natali Dubel
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Susanne Liese
- Institut für Theoretische Physik; Freie Universität Berlin; Arnimallee 14 14195 Berlin Deutschland
| | - Franziska Scherz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Oliver Seitz
- Institut für Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Deutschland
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Dubel N, Liese S, Scherz F, Seitz O. Exploring the Limits of Bivalency by DNA-Based Spatial Screening. Angew Chem Int Ed Engl 2018; 58:907-911. [DOI: 10.1002/anie.201810996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Natali Dubel
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Susanne Liese
- Institute for Theoretical Physics; Free University Berlin; Arnimallee 14 14195 Berlin Germany
| | - Franziska Scherz
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Oliver Seitz
- Institute of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 12489 Berlin Germany
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8
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: Switch-like, Light-Controlled Perturbations inside Living Cells. Angew Chem Int Ed Engl 2017; 56:5916-5920. [DOI: 10.1002/anie.201611432] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/10/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Muthukumaran Venkatachalapathy
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Dominic Kamps
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Simone Weigel
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Orlich
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Ruben Garrecht
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: schaltbare, lichtgesteuerte Manipulation in lebenden Zellen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Muthukumaran Venkatachalapathy
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Dominic Kamps
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Simone Weigel
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Ravi Kumar
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Orlich
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Ruben Garrecht
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Hirtz
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Christof M. Niemeyer
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Leif Dehmelt
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
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12
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Angelin A, Kassel O, Rastegar S, Strähle U, Niemeyer CM. Protein-Functionalized DNA Nanostructures as Tools to Control Transcription in Zebrafish Embryos. ChemistryOpen 2017; 6:33-39. [PMID: 28168148 PMCID: PMC5288758 DOI: 10.1002/open.201600153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Indexed: 01/02/2023] Open
Abstract
The unique structure-directing properties of DNA origami nanostructures (DONs) show great potential to specifically manipulate intracellular processes. We report an innovative concept to selectively activate the transcription of a single gene in the developing zebrafish embryo. We reason that engineering a designer transcription factor in which a rigid DON imposes a fixed distance between the DNA-binding domain (DBD) and the transactivation domain (TAD) would allow the selective activation of a gene harboring the same distance between the corresponding transcription factor binding site and the core promoter. As a test case, a rigid tubular DON was designed to separate the DBD of the GAL4 transcription factor and the VP16 viral protein as a TAD. This construct was microinjected in the yolk of one-cell-stage zebrafish embryos, together with a reporter plasmid to assess its functionality. The large DON was efficiently distributed to cells of the developing embryo and showed no signs of toxicity. However, because the DON showed only a cytosolic localization, it did not activate transcription of the reporter gene. Although this work clearly demonstrates that DON microinjection enables the intracellular distribution of multi-protein architectures in most of the cells of the developing zebrafish embryo, further refinements are necessary to enable selective gene activation in vivo.
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Affiliation(s)
- Alessandro Angelin
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Olivier Kassel
- Karlsruhe Institute of Technology (KIT)Institute for Toxicology and Genetics (ITG)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Sepand Rastegar
- Karlsruhe Institute of Technology (KIT)Institute for Toxicology and Genetics (ITG)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Uwe Strähle
- Karlsruhe Institute of Technology (KIT)Institute for Toxicology and Genetics (ITG)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
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Finke A, Bußkamp H, Manea M, Marx A. Durch Polymerase-Kettenreaktion erzeugte DNA-Peptid-Netzwerke als künstliche extrazelluläre Matrix. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Finke
- Fachbereich Chemie und Konstanz Research School, Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Holger Bußkamp
- Fachbereich Chemie und Konstanz Research School, Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Marilena Manea
- Fachbereich Chemie und Konstanz Research School, Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie und Konstanz Research School, Chemical Biology; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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Finke A, Bußkamp H, Manea M, Marx A. Designer Extracellular Matrix Based on DNA-Peptide Networks Generated by Polymerase Chain Reaction. Angew Chem Int Ed Engl 2016; 55:10136-40. [DOI: 10.1002/anie.201604687] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Alexander Finke
- Department of Chemistry and Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Holger Bußkamp
- Department of Chemistry and Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Marilena Manea
- Department of Chemistry and Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology; University of Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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15
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Garrecht R, Meyer R, Duppach J, Reipschläger S, Watzl C, Niemeyer CM. Designed DNA Surfaces for in Vitro Modulation of Natural Killer Cells. Chembiochem 2016; 17:486-92. [DOI: 10.1002/cbic.201500629] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Ruben Garrecht
- Karlsruhe Institute of Technology (KIT); Institute for Biological Interfaces (IBG 1); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Rebecca Meyer
- Karlsruhe Institute of Technology (KIT); Institute for Biological Interfaces (IBG 1); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Janine Duppach
- Leibniz Research Center for Working Environment and Human Factors (IfADo) at TU Dortmund; Ardeystrasse 67 44139 Dortmund Germany
| | - Simone Reipschläger
- Leibniz Research Center for Working Environment and Human Factors (IfADo) at TU Dortmund; Ardeystrasse 67 44139 Dortmund Germany
| | - Carsten Watzl
- Leibniz Research Center for Working Environment and Human Factors (IfADo) at TU Dortmund; Ardeystrasse 67 44139 Dortmund Germany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT); Institute for Biological Interfaces (IBG 1); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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