1
|
Henkel M, Kimna C, Lieleg O. DNA Crosslinked Mucin Hydrogels Allow for On-Demand Gel Disintegration and Triggered Particle Release. Macromol Biosci 2024; 24:e2300427. [PMID: 38217373 DOI: 10.1002/mabi.202300427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/04/2023] [Indexed: 01/15/2024]
Abstract
Whereas hydrogels created from synthetic polymers offer a high level of control over their stability and mechanical properties, their biomedical activity is typically limited. In contrast, biopolymers have evolved over billions of years to integrate a broad range of functionalities into a single design. Thus, biopolymeric hydrogels can show remarkable capabilities such as regulatory behavior, selective barrier properties, or antimicrobial effects. Still, despite their widespread use in numerous biomedical applications, achieving a meticulous control over the physical properties of macroscopic biopolymeric networks remains a challenge. Here, a macroscopic, DNA-crosslinked mucin hydrogel with tunable viscoelastic properties that responds to two types of triggers: temperature alterations and DNA displacement strands, is presented. As confirmed with bulk rheology and single particle tracking, the hybridized base pairs governing the stability of the hydrogel can be opened, thus allowing for a precise control over the hydrogel stiffness and even enabling a full gel-to-sol transition. As those DNA-crosslinked mucin hydrogels possess tunable mechanical properties and can be disintegrated on demand, they can not only be considered for controlled cargo release but may also serve as a role model for the development of smart biomedical materials in applications such as tissue engineering and wound healing.
Collapse
Affiliation(s)
- Manuel Henkel
- School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
- Center for Protein Assemblies (CPA) and Munich Institute of Biomedical Engineering, Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Ceren Kimna
- School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
- Center for Protein Assemblies (CPA) and Munich Institute of Biomedical Engineering, Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Oliver Lieleg
- School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
- Center for Protein Assemblies (CPA) and Munich Institute of Biomedical Engineering, Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| |
Collapse
|
2
|
Jorgenson TD, Baboolall KD, Suarez C, Kovar DR, Gardel ML, Rowan SJ. Highly flexible PEG-LifeAct constructs act as tunable biomimetic actin crosslinkers. SOFT MATTER 2024; 20:971-977. [PMID: 38190228 PMCID: PMC10828923 DOI: 10.1039/d3sm01341c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
In vitro studies of actin filament networks crosslinked with dynamic actin binding proteins provide critical insights into cytoskeletal mechanics as well as inspiration for new adaptive materials design. However, discontinuous variance in the physiochemical properties of actin binding proteins impedes holistic relationships between crosslinker molecular parameters, network structure, and mechanics. Bio-synthetic constructs composed of synthetic polymer backbones and actin binding motifs would enable crosslinkers with engineered physiochemical properties to directly target the desired structure-property relationships. As a proof of concept, bio-synthetic crosslinkers composed of highly flexible polyethylene glycol (PEG) polymers functionalized with the actin binding peptide LifeAct, are explored as actin crosslinkers. Using bulk rheology and fluorescence microscopy, these constructs are shown to modulate actin filament network structure and mechanics in a contour length dependent manner, while maintaining the stress-stiffening behavior inherent to actin filament networks. These results encourage the design of more diverse and complex peptide-polymer crosslinkers to interrogate and control semi-flexible polymer networks.
Collapse
Affiliation(s)
- Tyler D Jorgenson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
| | | | - Cristian Suarez
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Margaret L Gardel
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- James Franck Institute, University of Chicago, Chicago, IL, USA
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Stuart J Rowan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| |
Collapse
|
3
|
Peng YH, Hsiao SK, Gupta K, Ruland A, Auernhammer GK, Maitz MF, Boye S, Lattner J, Gerri C, Honigmann A, Werner C, Krieg E. Dynamic matrices with DNA-encoded viscoelasticity for cell and organoid culture. NATURE NANOTECHNOLOGY 2023; 18:1463-1473. [PMID: 37550574 PMCID: PMC10716043 DOI: 10.1038/s41565-023-01483-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Three-dimensional cell and organoid cultures rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack control over key cell-instructive properties. Here we report on fully synthetic hydrogels based on DNA libraries that self-assemble with ultrahigh-molecular-weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables computationally predictable and systematic control over its viscoelasticity, thermodynamic and kinetic parameters by changing DNA sequence information. Adjustable heat activation allows homogeneous embedding of mammalian cells. Intriguingly, stress-relaxation times can be tuned over four orders of magnitude, recapitulating mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto- and haemocompatibility, and controllable degradation. DyNAtrix-based cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts and human trophoblast organoids show high viability, proliferation and morphogenesis. DyNAtrix thus represents a programmable and versatile precision matrix for advanced approaches to biomechanics, biophysics and tissue engineering.
Collapse
Affiliation(s)
- Yu-Hsuan Peng
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Syuan-Ku Hsiao
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Krishna Gupta
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - André Ruland
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Günter K Auernhammer
- Institute for Physical Chemistry and Polymer Physics, Polymer Interfaces, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Manfred F Maitz
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Susanne Boye
- Institute for Macromolecular Chemistry, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Johanna Lattner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Claudia Gerri
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Carsten Werner
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Elisha Krieg
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany.
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
4
|
Mollenkopf P, Prascevic D, Bayerl TM, Käs JA, Schnauß J. Heavy water induces bundling in entangled actin networks. RSC Adv 2023; 13:24795-24800. [PMID: 37601592 PMCID: PMC10437092 DOI: 10.1039/d3ra03917j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023] Open
Abstract
Heavy water is known to affect many different biological systems, with the most striking effects observed at the cellular level. Many dynamic processes, such as migration or invasion, but also central processes of cell proliferation are measurably inhibited by the presence of deuterium oxide (D2O). Furthermore, individual cell deformabilities are significantly decreased upon D2O treatment. In order to understand the origin of these effects, we studied entangled filamentous actin networks, a commonly used model system for the cytoskeleton, which is considered a central functional element for dynamic cellular processes. Using bulk shear rheology to extract rheological signatures of reconstituted actin networks at varying concentrations of D2O, we found a non-monotonic behavior, which is explainable by a drastic change in the actin network architecture. Applying light scattering and fluorescence microscopy, we were able to demonstrate that the presence of deuterium oxide induces bundling in reconstituted entangled networks of filamentous actin. This constitutes an entirely novel and previously undescribed actin bundling mechanism.
Collapse
Affiliation(s)
- Paul Mollenkopf
- Department of Physiology, University of Pennsylvania Philadelphia PA 19104 USA
| | - Dusan Prascevic
- Peter-Debye Institute for Soft Matter Physics, Leipzig University 04103 Leipzig Germany
| | - Thomas M Bayerl
- Inventages 16 Northfields Prospect Business Centre, Putney Bridge Rd London SW181PE UK
| | - Josef A Käs
- Peter-Debye Institute for Soft Matter Physics, Leipzig University 04103 Leipzig Germany
| | - Jörg Schnauß
- Peter-Debye Institute for Soft Matter Physics, Leipzig University 04103 Leipzig Germany
- Fraunhofer Institute for Cell Therapy and Immunology 04103 Leipzig Germany
- Unconventional Computing Lab, Department of Computer Science and Creative Technologies, University of the West of England Bristol BS16 1QY UK
| |
Collapse
|
5
|
Freitag JS, Möser C, Belay R, Altattan B, Grasse N, Pothineni BK, Schnauß J, Smith DM. Integration of functional peptides into nucleic acid-based nanostructures. NANOSCALE 2023; 15:7608-7624. [PMID: 37042085 DOI: 10.1039/d2nr05429a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In many applications such as diagnostics and therapy development, small peptide fragments consisting of only a few amino acids are often attractive alternatives to bulky proteins. This is due to factors such as the ease of scalable chemical synthesis and numerous methods for their discovery. One drawback of using peptides is that their activity can often be negatively impacted by the lack of a rigid, 3D stabilizing structure provided by the rest of the protein. In many cases, this can be alleviated by different methods of rational templating onto nanomaterials, which provides additional possibilities to use concepts of multivalence or rational nano-engineering to enhance or even create new types of function or structure. In recent years, nanostructures made from the self-assembly of DNA strands have been used as scaffolds to create functional arrangements of peptides, often leading to greatly enhanced biological activity or new material properties. This review will give an overview of nano-templating approaches based on the combination of DNA nanotechnology and peptides. This will include both bioengineering strategies to control interactions with cells or other biological systems, as well as examples where the combination of DNA and peptides has been leveraged for the rational design of new functional materials.
Collapse
Affiliation(s)
- Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Christin Möser
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Robel Belay
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Basma Altattan
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Nico Grasse
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | | | - Jörg Schnauß
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Unconventional Computing Lab, UWE, Bristol, BS16 1QY, UK
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
| |
Collapse
|
6
|
Glaser M, Mollenkopf P, Prascevic D, Ferraz C, Käs JA, Schnauß J, Smith DM. Systematic altering of semiflexible DNA-based polymer networks via tunable crosslinking. NANOSCALE 2023; 15:7374-7383. [PMID: 37039012 PMCID: PMC10134436 DOI: 10.1039/d2nr05615a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
In order to understand and predict the mechanical behaviours of complex, soft biomaterials such as cells or stimuli-responsive hydrogels, it is important to connect how the nanoscale properties of their constituent components impact those of the bulk material. Crosslinked networks of semiflexible polymers are particularly ubiquitous, being underlying mechanical components of biological systems such as cells or ECM, as well as many synthetic or biomimetic materials. Cell-derived components such as filamentous biopolymers or protein crosslinkers are readily available and well-studied model systems. However, as evolutionarily derived materials, they are constrained to a fixed set of structural parameters such as the rigidity and size of the filaments, or the valency and strength of binding of crosslinkers forming inter-filament connections. By implementing a synthetic model system based on the self-assembly of DNA oligonucleotides into nanometer-scale tubes and simple crosslinking constructs, we used the thermodynamic programmability of DNA hybridization to explore the impact of binding affinity on bulk mechanical response. Stepwise tuning the crosslinking affinity over a range from transient to thermodynamically stable shows an according change in viscoelastic behaviour from loosely entangled to elastic, consistent with models accounting for generalized inter-filament interactions. While characteristic signatures of concentration-dependent changes in network morphology found in some other natural and synthetic filament-crosslinker systems were not apparent, the presence of a distinct elasticity increase within a narrow range of conditions points towards potential subtle alterations of crosslink-filament architecture. Here, we demonstrate a new synthetic approach for gaining a deeper understanding of both biological as well as engineered hydrogel systems.
Collapse
Affiliation(s)
- Martin Glaser
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
- Soft Matter Physics Division, Peter Debye Institute, Faculty of Physics and Earth Sciences, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany
| | - Paul Mollenkopf
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
- Soft Matter Physics Division, Peter Debye Institute, Faculty of Physics and Earth Sciences, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany
| | - Dusan Prascevic
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
| | - Catarina Ferraz
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
- Soft Matter Physics Division, Peter Debye Institute, Faculty of Physics and Earth Sciences, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany
| | - Josef A Käs
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
| | - Jörg Schnauß
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
- Soft Matter Physics Division, Peter Debye Institute, Faculty of Physics and Earth Sciences, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany
| | - David M Smith
- DNA Nanodevices Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany.
- Soft Matter Physics Division, Peter Debye Institute, Faculty of Physics and Earth Sciences, Leipzig University, Linnéstr. 5, 04103 Leipzig, Germany
| |
Collapse
|
7
|
Dwyer ME, Robertson-Anderson RM, Gurmessa BJ. Nonlinear Microscale Mechanics of Actin Networks Governed by Coupling of Filament Crosslinking and Stabilization. Polymers (Basel) 2022; 14:polym14224980. [PMID: 36433106 PMCID: PMC9696012 DOI: 10.3390/polym14224980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Actin plays a vital role in maintaining the stability and rigidity of biological cells while allowing for cell motility and shape change. The semiflexible nature of actin filaments-along with the myriad actin-binding proteins (ABPs) that serve to crosslink, bundle, and stabilize filaments-are central to this multifunctionality. The effect of ABPs on the structural and mechanical properties of actin networks has been the topic of fervent investigation over the past few decades. Yet, the combined impact of filament stabilization, stiffening and crosslinking via ABPs on the mechanical response of actin networks has yet to be explored. Here, we perform optical tweezers microrheology measurements to characterize the nonlinear force response and relaxation dynamics of actin networks in the presence of varying concentrations of α-actinin, which transiently crosslinks actin filaments, and phalloidin, which stabilizes filamentous actin and increases its persistence length. We show that crosslinking and stabilization can act both synergistically and antagonistically to tune the network resistance to nonlinear straining. For example, phalloidin stabilization leads to enhanced elastic response and reduced dissipation at large strains and timescales, while the initial microscale force response is reduced compared to networks without phalloidin. Moreover, we find that stabilization switches this initial response from that of stress stiffening to softening despite the increased filament stiffness that phalloidin confers. Finally, we show that both crosslinking and stabilization are necessary to elicit these emergent features, while the effect of stabilization on networks without crosslinkers is much more subdued. We suggest that these intriguing mechanical properties arise from the competition and cooperation between filament connectivity, bundling, and rigidification, shedding light on how ABPs with distinct roles can act in concert to mediate diverse mechanical properties of the cytoskeleton and bio-inspired polymeric materials.
Collapse
Affiliation(s)
- Mike E. Dwyer
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA 17837, USA
| | | | - Bekele J. Gurmessa
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA 17837, USA
- Correspondence:
| |
Collapse
|
8
|
Spukti FF, Schnauß J. Large and stable: actin aster networks formed via entropic forces. Front Chem 2022; 10:899478. [PMID: 36118308 PMCID: PMC9481034 DOI: 10.3389/fchem.2022.899478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Biopolymer networks play a major role as part of the cytoskeleton. They provide stable structures and act as a medium for signal transport. These features encourage the application of such networks as organic computation devices. While research on this topic is not advanced yet, previous results are very promising. The protein actin in particular appears advantageous. It can be arranged to various stable structures and transmit several signals. In this study aster shaped networks were self-assembled via entropic forces by the crowding agent methyl cellulose. These networks are characterised by a regular and uniquely thick bundle structure, but have so far only been accounted in droplets of 100 μm diameter. We report now regular asters in an area of a few mm2 that could be observed even after months. Such stability outside of an organism is striking and underlines the great potential actin aster networks display.
Collapse
Affiliation(s)
| | - Jörg Schnauß
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, United Kingdom
| |
Collapse
|
9
|
Characterization of binding interactions of SARS-CoV-2 spike protein and DNA-peptide nanostructures. Sci Rep 2022; 12:12828. [PMID: 35896714 PMCID: PMC9328006 DOI: 10.1038/s41598-022-16914-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/15/2022] [Indexed: 12/22/2022] Open
Abstract
Binding interactions of the spike proteins of the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) to a peptide fragment derived from the human angiotensin converting enzyme 2 (hACE2) receptor are investigated. The peptide is employed as capture moiety in enzyme linked immunosorbent assays (ELISA) and quantitative binding interaction measurements that are based on fluorescence proximity sensing (switchSENSE). In both techniques, the peptide is presented on an oligovalent DNA nanostructure, in order to assess the impact of mono- versus trivalent binding modes. As the analyte, the spike protein and several of its subunits are tested as well as inactivated SARS-CoV-2 and pseudo viruses. While binding of the peptide to the full-length spike protein can be observed, the subunits RBD and S1 do not exhibit binding in the employed concentrations. Variations of the amino acid sequence of the recombinant full-length spike proteins furthermore influence binding behavior. The peptide was coupled to DNA nanostructures that form a geometric complement to the trimeric structure of the spike protein binding sites. An increase in binding strength for trimeric peptide presentation compared to single peptide presentation could be generally observed in ELISA and was quantified in switchSENSE measurements. Binding to inactivated wild type viruses could be shown as well as qualitatively different binding behavior of the Alpha and Beta variants compared to the wild type virus strain in pseudo virus models.
Collapse
|
10
|
Cao D, Xie Y, Song J. DNA Hydrogels in the Perspective of Mechanical Properties. Macromol Rapid Commun 2022; 43:e2200281. [PMID: 35575627 DOI: 10.1002/marc.202200281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/25/2022] [Indexed: 11/10/2022]
Abstract
Tailoring the mechanical properties has always been a key to the field of hydrogels in terms of different applications. Particularly, deoxyribonucleic acid (DNA) hydrogels offer an unambiguous way to precisely tune the mechanical properties, largely on account of their programmable sequences, abundant responding toolbox, and various ligation approaches. In this review, DNA hydrogels from the perspective of mechanical properties, from synthetic standpoint to different applications are introduced. The relationship between the structure and their mechanical properties in DNA hydrogels and the methods of regulating the mechanical properties of DNA hydrogels are specifically summarized. Furthermore, several recent applications of DNA hydrogels in relation to their mechanical properties are discussed. Benefiting from the tunability and flexibility, rational design of mechanical properties in DNA hydrogels provided unheralded interest from fundamental science to extensive applications. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Dengjie Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| |
Collapse
|
11
|
Constraint Release for Reptating Filaments in Semiflexible Networks Depends on Background Fluctuations. Polymers (Basel) 2022; 14:polym14040707. [PMID: 35215620 PMCID: PMC8879693 DOI: 10.3390/polym14040707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Entangled semiflexible polymer networks are usually described by the tube model, although this concept has not been able to explain all experimental observations. One of its major shortcomings is neglecting the thermal fluctuations of the polymers surrounding the examined test filament, such that disentanglement effects are not captured. In this study, we present experimental evidence that correlated constraint release which has been predicted theoretically occurs in entangled, but not in crosslinked semiflexible polymer networks. By tracking single semiflexible DNA nanotubes embedded both in entangled and crosslinked F-actin networks, we observed different reptation dynamics in both systems, emphasizing the need for a revision of the classical tube theory for entangled polymer solutions.
Collapse
|
12
|
Elbalasy I, Wilharm N, Herchenhahn E, Konieczny R, Mayr SG, Schnauß J. From Strain Stiffening to Softening—Rheological Characterization of Keratins 8 and 18 Networks Crosslinked via Electron Irradiation. Polymers (Basel) 2022; 14:polym14030614. [PMID: 35160604 PMCID: PMC8838340 DOI: 10.3390/polym14030614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
Networks of crosslinked keratin filaments are abundant in epithelial cells and tissues, providing resilience against mechanical forces and ensuring cellular integrity. Although studies of in vitro models of reconstituted keratin networks have revealed important mechanical aspects, the mechanical properties of crosslinked keratin structures remain poorly understood. Here, we exploited the power of electron beam irradiation (EBI) to crosslink in vitro networks of soft epithelial keratins 8 and 18 (k8–k18) filaments with different irradiation doses (30 kGy, 50 kGy, 80 kGy, 100 kGy, and 150 kGy). We combined bulk shear rheology with confocal microscopy to investigate the impact of crosslinking on the mechanical and structural properties of the resultant keratin gels. We found that irradiated keratin gels display higher linear elastic modulus than the unirradiated, entangled networks at all doses tested. However, at the high doses (80 kGy, 100 kGy, and 150 kGy), we observed a remarkable drop in the elastic modulus compared to 50 kGy. Intriguingly, the irradiation drastically changed the behavior for large, nonlinear deformations. While untreated keratin networks displayed a strong strain stiffening, increasing irradiation doses shifted the system to a strain softening behavior. In agreement with the rheological behavior in the linear regime, the confocal microscopy images revealed fully isotropic networks with high percolation in 30 kGy and 50 kGy-treated keratin samples, while irradiation with 100 kGy induced the formation of thick bundles and clusters. Our results demonstrate the impact of permanent crosslinking on k8–k18 mechanics and provide new insights into the potential contribution of intracellular covalent crosslinking to the loss of mechanical resilience in some human keratin diseases. These insights will also provide inspiration for the synthesis of new keratin-based biomaterials.
Collapse
Affiliation(s)
- Iman Elbalasy
- Peter-Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Faculty of Science, Cairo University, Giza 12613, Egypt
- Correspondence: (I.E.); (S.G.M.); (J.S.)
| | - Nils Wilharm
- Leibniz-Institut für Oberflächenmodifizierung e.V. (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (N.W.); (R.K.)
- Division of Surface Physics, Department of Physics and Earth Sciences, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
| | - Erik Herchenhahn
- Peter-Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
| | - Robert Konieczny
- Leibniz-Institut für Oberflächenmodifizierung e.V. (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (N.W.); (R.K.)
| | - Stefan G. Mayr
- Leibniz-Institut für Oberflächenmodifizierung e.V. (IOM), Permoserstr. 15, 04318 Leipzig, Germany; (N.W.); (R.K.)
- Division of Surface Physics, Department of Physics and Earth Sciences, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
- Correspondence: (I.E.); (S.G.M.); (J.S.)
| | - Jörg Schnauß
- Peter-Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
- Unconventional Computing Lab, Department of Computer Science and Creative Technologies, UWE, Bristol BS16 1QY, UK
- Correspondence: (I.E.); (S.G.M.); (J.S.)
| |
Collapse
|
13
|
Affiliation(s)
- Dong Wang
- Department of Biological and Environmental Engineering Cornell University Ithaca New York 14853 USA
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Micro-Nano Research and Diagnosis Center Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Dan Luo
- Department of Biological and Environmental Engineering Cornell University Ithaca New York 14853 USA
- Kavli Institute at Cornell for Nanoscale Science Cornell University Ithaca New York 14853 USA
| |
Collapse
|
14
|
Wang D, Liu P, Luo D. Putting DNA to Work as Generic Polymeric Materials. Angew Chem Int Ed Engl 2021; 61:e202110666. [PMID: 34545660 DOI: 10.1002/anie.202110666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Indexed: 01/10/2023]
Abstract
DNA is a true polymer that stores the genetic information of an organism. With its amazing biological and polymeric characteristics, DNA has been regarded as a universal building block for the construction of diverse materials for real-world applications. Through various approaches including ligation, polymerization, chemical crosslinking, and physical crosslinking, both pure and hybrid DNA gels have been developed as generic materials. This Review discusses recent advances in the construction of DNA-based networks without considering any of DNA's genetic properties. In addition, we highlight the biomedical and non-biomedical applications of DNA as generic materials. Owing to the superb molecular recognition, self-assembly, and responsiveness of DNA, a mushrooming number of DNA materials with various properties have been developed for general utilization.
Collapse
Affiliation(s)
- Dong Wang
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, 14853, USA
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, China.,Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, 14853, USA.,Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York, 14853, USA
| |
Collapse
|
15
|
Schnauß J, Kunschmann T, Grosser S, Mollenkopf P, Zech T, Freitag JS, Prascevic D, Stange R, Röttger LS, Rönicke S, Smith DM, Bayerl TM, Käs JA. Cells in Slow Motion: Apparent Undercooling Increases Glassy Behavior at Physiological Temperatures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101840. [PMID: 34085345 DOI: 10.1002/adma.202101840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Solvent conditions are unexpectedly sufficient to drastically and reversibly slow down cells. In vitro on the molecular level, protein-solvent interactions drastically change in the presence of heavy water (D2 O) and its stronger hydrogen bonds. Adding D2 O to the cell medium of living cells increases the molecular intracellular viscosity. While cell morphology and phenotype remain unchanged, cellular dynamics transform into slow motion in a changeable manner. This is exemplified in the slowdown of cell proliferation and migration, which is caused by a reversible gelation of the cytoplasm. In analogy to the time-temperature superposition principle, where temperature is replaced by D2 O, an increase in viscosity slows down the effective time. Actin networks, crucial structures in the cytoplasm, switch from a power-law-like viscoelastic to a more rubber-like elastic behavior. The resulting intracellular resistance and dissipation impair cell movement. Since cells are highly adaptive non-equilibrium systems, they usually respond irreversibly from a thermodynamic perspective. D2 O induced changes, however, are fully reversible and their effects are independent of signaling as well as expression. The stronger hydrogen bonds lead to glass-like, drawn-out intramolecular dynamics, which may facilitate longer storage times of biological matter, for instance, during transport of organ transplants.
Collapse
Affiliation(s)
- Jörg Schnauß
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
- Unconventional Computing Lab, Department of Computer Science and Creative Technologies, University of the West of England, Bristol, BS16 1QY, UK
| | - Tom Kunschmann
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
| | - Steffen Grosser
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
| | - Paul Mollenkopf
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Tobias Zech
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7BE, UK
| | - Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
| | - Dusan Prascevic
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
| | - Roland Stange
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
| | - Luisa S Röttger
- D2 Bioscience Group Ltd, Trinity Hall, 43 Cedar Ave., Hamilton, HM LX, Bermuda
| | - Susanne Rönicke
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
| | - David M Smith
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103, Leipzig, Germany
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar, 382007, India
| | - Thomas M Bayerl
- D2 Bioscience Group Ltd, Trinity Hall, 43 Cedar Ave., Hamilton, HM LX, Bermuda
| | - Josef A Käs
- Peter Debye Institute for Soft Matter Physics, University Leipzig, Linnéstraße 5, 04103, Leipzig, Germany
| |
Collapse
|
16
|
Händler T, Tutmarc C, Glaser M, Freitag JS, Smith DM, Schnauß J. Measuring structural parameters of crosslinked and entangled semiflexible polymer networks with single-filament tracing. Phys Rev E 2021; 103:062501. [PMID: 34271634 DOI: 10.1103/physreve.103.062501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/17/2021] [Indexed: 12/15/2022]
Abstract
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular interactions with the surrounding network impacts the measurement of these parameters has not been possible with the established experimental systems. Here we use mechanically programmable DNA nanotubes embedded in crosslinked and entangled F-actin networks, as well as in synthetic DNA networks, in order to measure fundamental, structural network properties like tube width and mesh size with respect to the stiffness of the tracers. While we confirm some predictions derived from models based purely on steric interactions, our results indicate that these models should be expanded to account for additional interfilament interactions, thereby describing the behavior of real polymer networks.
Collapse
Affiliation(s)
- Tina Händler
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Cary Tutmarc
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Martin Glaser
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - David M Smith
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany.,Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India
| | - Jörg Schnauß
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany.,Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, United Kingdom
| |
Collapse
|
17
|
Smith DM, Keller A. DNA Nanostructures in the Fight Against Infectious Diseases. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000049. [PMID: 33615315 PMCID: PMC7883073 DOI: 10.1002/anbr.202000049] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.
Collapse
Affiliation(s)
- David M. Smith
- DNA Nanodevices UnitDepartment DiagnosticsFraunhofer Institute for Cell Therapy and Immunology IZI04103LeipzigGermany
- Peter Debye Institute for Soft Matter PhysicsFaculty of Physics and Earth SciencesUniversity of Leipzig04103LeipzigGermany
- Institute of Clinical ImmunologyUniversity of Leipzig Medical School04103LeipzigGermany
- Dhirubhai Ambani Institute of Information and Communication TechnologyGandhinagar382 007India
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| |
Collapse
|
18
|
Naomi R, Fauzi MB. Cellulose/Collagen Dressings for Diabetic Foot Ulcer: A Review. Pharmaceutics 2020; 12:E881. [PMID: 32957476 PMCID: PMC7558961 DOI: 10.3390/pharmaceutics12090881] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Diabetic foot ulcer (DFU) is currently a global concern and it requires urgent attention, as the cost allocation by the government for DFU increases every year. This review was performed to provide scientific evidence on the advanced biomaterials that can be utilised as a first-line treatment for DFU patients. Cellulose/collagen dressings have a biological property on non-healing wounds, such as DFU. This review aims to analyse scientific-based evidence of cellulose/collagen dressing for DFU. It has been proven that the healing rate of cellulose/collagen dressing for DFU patients demonstrated a significant improvement in wound closure as compared to current standard or conventional dressings. It has been scientifically proven that cellulose/collagen dressing provides a positive effect on non-healing DFU. There is a high tendency for cellulose/collagen dressing to be used, as it highly promotes angiogenesis with a rapid re-epithelisation rate that has been proven effective in clinical trials.
Collapse
Affiliation(s)
| | - Mh Busra Fauzi
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia;
| |
Collapse
|
19
|
Schnauß J, Schmidt BUS, Brazel CB, Dogan S, Losert W, Anderegg U, Käs JA. Influence of hyaluronic acid binding on the actin cortex measured by optical forces. JOURNAL OF BIOPHOTONICS 2020; 13:e201960215. [PMID: 32246559 DOI: 10.1002/jbio.201960215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Melanoma cells are often surrounded by hyaluronic acid (HA) rich environments, which are considered to promote tumor progression and metastasis. Induced effects in compound materials consisting of cells embedded in an extracellular matrix have been studied, however, alterations of the single cells have never been addressed. Here, we explicitly addressed single cell properties and measured HA-induced biomechanical changes via deformations induced solely by optical forces. With the optical stretcher setup, cells were deformed after culturing them in either the presence or absence of HA revealing the crucial interplay of HA with the CD44 receptor. To assess the role of CD44 in transducing effects of HA, we compared a CD44 expressing variant of the melanoma cell line RPM-MC to its natural CD44-negative counterpart. Our measurements revealed a significant stiffness change, which we attribute to changes of the actin cytoskeleton.
Collapse
Affiliation(s)
- Jörg Schnauß
- Leipzig University, Faculty of Physics and Earth Sciences, Peter Debye Institute for Soft Matter Physics, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - B U Sebastian Schmidt
- University of Maryland, Institute for Physical Science and Technology, Physical Sciences Complex, College Park, MD, USA
| | - Christina B Brazel
- Department of Dermatology, Leipzig University, Medical Faculty, Leipzig, Germany
| | - Senol Dogan
- Leipzig University, Faculty of Physics and Earth Sciences, Peter Debye Institute for Soft Matter Physics, Leipzig, Germany
| | - Wolfgang Losert
- University of Maryland, Institute for Physical Science and Technology, Physical Sciences Complex, College Park, MD, USA
| | - Ulf Anderegg
- Department of Dermatology, Leipzig University, Medical Faculty, Leipzig, Germany
| | - Josef A Käs
- Leipzig University, Faculty of Physics and Earth Sciences, Peter Debye Institute for Soft Matter Physics, Leipzig, Germany
| |
Collapse
|
20
|
Grad EM, Tunn I, Voerman D, de Léon AS, Hammink R, Blank KG. Influence of Network Topology on the Viscoelastic Properties of Dynamically Crosslinked Hydrogels. Front Chem 2020; 8:536. [PMID: 32719773 PMCID: PMC7349520 DOI: 10.3389/fchem.2020.00536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/26/2020] [Indexed: 01/15/2023] Open
Abstract
Biological materials combine stress relaxation and self-healing with non-linear stress-strain responses. These characteristic features are a direct result of hierarchical self-assembly, which often results in fiber-like architectures. Even though structural knowledge is rapidly increasing, it has remained a challenge to establish relationships between microscopic and macroscopic structure and function. Here, we focus on understanding how network topology determines the viscoelastic properties, i.e., stress relaxation, of biomimetic hydrogels. We have dynamically crosslinked two different synthetic polymers with one and the same crosslink. The first polymer, a polyisocyanopeptide (PIC), self-assembles into semi-flexible, fiber-like bundles, and thus displays stress-stiffening, similar to many biopolymer networks. The second polymer, 4-arm poly(ethylene glycol) (starPEG), serves as a reference network with well-characterized structural and viscoelastic properties. Using one and the same coiled coil crosslink allows us to decouple the effects of crosslink kinetics and network topology on the stress relaxation behavior of the resulting hydrogel networks. We show that the fiber-containing PIC network displays a relaxation time approximately two orders of magnitude slower than the starPEG network. This reveals that crosslink kinetics is not the only determinant for stress relaxation. Instead, we propose that the different network topologies determine the ability of elastically active network chains to relax stress. In the starPEG network, each elastically active chain contains exactly one crosslink. In the absence of entanglements, crosslink dissociation thus relaxes the entire chain. In contrast, each polymer is crosslinked to the fiber bundle in multiple positions in the PIC hydrogel. The dissociation of a single crosslink is thus not sufficient for chain relaxation. This suggests that tuning the number of crosslinks per elastically active chain in combination with crosslink kinetics is a powerful design principle for tuning stress relaxation in polymeric materials. The presence of a higher number of crosslinks per elastically active chain thus yields materials with a slow macroscopic relaxation time but fast dynamics at the microscopic level. Using this principle for the design of synthetic cell culture matrices will yield materials with excellent long-term stability combined with the ability to locally reorganize, thus facilitating cell motility, spreading, and growth.
Collapse
Affiliation(s)
- Emilia M. Grad
- Mechano(bio) Chemistry, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
| | - Isabell Tunn
- Mechano(bio) Chemistry, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Dion Voerman
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alberto S. de Léon
- Mechano(bio) Chemistry, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Roel Hammink
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kerstin G. Blank
- Mechano(bio) Chemistry, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
| |
Collapse
|
21
|
Siccardi S, Adamatzky A, Tuszyński J, Huber F, Schnauß J. Actin networks voltage circuits. Phys Rev E 2020; 101:052314. [PMID: 32575228 DOI: 10.1103/physreve.101.052314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/28/2020] [Indexed: 11/07/2022]
Abstract
Filaments of the cellular protein actin can form bundles, which can conduct ionic currents as well as mechanical and voltage solitons. These inherent properties can be utilized to generate computing circuits solely based on self-assembled actin bundle structures. Starting with experimentally observed networks of actin bundles, we model their network structure in terms of edges and nodes. We compute and discuss the main electrical parameters, considering the bundles as electrical wires with either low or high filament densities. A set of equations describing the network is solved with several initial conditions. Input voltages, which can be considered as information bits, are applied in a set of points and output voltages are computed in another set of positions. We consider both an idealized situation, where pointlike electrodes can be inserted in any points of the bundles and a more realistic case, where electrodes lay on a surface and have typical dimensions available in the industry. We find that in both cases such a system can implement the main logical gates and a finite state machine.
Collapse
Affiliation(s)
- Stefano Siccardi
- Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, United Kingdom
| | - Andrew Adamatzky
- Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, United Kingdom
| | - Jack Tuszyński
- Department of Oncology, University of Alberta, Edmonton, Canada AB T6G 1Z2 and DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, TO, Turin, Italy
| | - Florian Huber
- Netherlands eScience Center, Science Park 140, 1098 XG Amsterdam, The Netherlands
| | - Jörg Schnauß
- Soft Matter Physics Division, Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, Leipzig University, Germany and Fraunhofer Institute for Cell Therapy and Immunology (IZI), DNA Nanodevices Group, Leipzig, Germany
| |
Collapse
|
22
|
Adamatzky A, Schnauß J, Huber F. Actin droplet machine. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191135. [PMID: 31903204 PMCID: PMC6936293 DOI: 10.1098/rsos.191135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 11/04/2019] [Indexed: 05/06/2023]
Abstract
The actin droplet machine is a computer model of a three-dimensional network of actin bundles developed in a droplet of a physiological solution, which implements mappings of sets of binary strings. The actin bundle network is conductive to travelling excitations, i.e. impulses. The machine is interfaced with an arbitrary selected set of k electrodes through which stimuli, binary strings of length k represented by impulses generated on the electrodes, are applied and responses are recorded. The responses are recorded in a form of impulses and then converted to binary strings. The machine's state is a binary string of length k: if there is an impulse recorded on the ith electrode, there is a '1' in the ith position of the string, and '0' otherwise. We present a design of the machine and analyse its state transition graphs. We envisage that actin droplet machines could form an elementary processor of future massive parallel computers made from biopolymers.
Collapse
Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, UK
| | - Jörg Schnauß
- Soft Matter Physics Division, Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, Leipzig University, Germany & Fraunhofer Institute for Cell Therapy and Immunology (IZI), DNA Nanodevices Unit, Leipzig, Germany
| | - Florian Huber
- Netherlands eScience Center, Science Park 140, 1098 XG Amsterdam, The Netherlands
| |
Collapse
|
23
|
Abstract
Actin filaments are conductive to ionic currents, mechanical and voltage solitons. These travelling localisations can be utilised to generate computing circuits from actin networks. The propagation of localisations on a single actin filament is experimentally unfeasible to control. Therefore, we consider excitation waves propagating on bundles of actin filaments. In computational experiments with a two-dimensional slice of an actin bundle network we show that by using an arbitrary arrangement of electrodes, it is possible to implement two-inputs-one-output circuits.
Collapse
Affiliation(s)
- Andrew Adamatzky
- Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, UK.
| | - Florian Huber
- Netherlands eScience Center, Science Park 140, 1098 XG, Amsterdam, The Netherlands
| | - Jörg Schnauß
- Soft Matter Physics Division, Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, Leipzig University, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), DNA Nanodevices Group, Leipzig, Germany
| |
Collapse
|
24
|
Cao XZ, Forest MG. Rheological Tuning of Entangled Polymer Networks by Transient Cross-links. J Phys Chem B 2019; 123:974-982. [DOI: 10.1021/acs.jpcb.8b09357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Xue-Zheng Cao
- Department of Mathematics and Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - M. Gregory Forest
- Department of Mathematics and Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
25
|
Möser C, Lorenz JS, Sajfutdinow M, Smith DM. Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence. Int J Mol Sci 2018; 19:ijms19113482. [PMID: 30404153 PMCID: PMC6274923 DOI: 10.3390/ijms19113482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2’s natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways.
Collapse
Affiliation(s)
- Christin Möser
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany.
- Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476 Potsdam, Germany.
| | - Jessica S Lorenz
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103 Leipzig, Germany.
| | - Martin Sajfutdinow
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany.
- Fraunhofer Project Center "Microelectronic and Optical Systems for Biomedicine" (MEOS), 99099 Erfurt, Germany.
| | - David M Smith
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103 Leipzig, Germany.
| |
Collapse
|