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Mohsenin H, Wagner HJ, Rosenblatt M, Kemmer S, Drepper F, Huesgen P, Timmer J, Weber W. Design of a Biohybrid Materials Circuit with Binary Decoder Functionality. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308092. [PMID: 38118057 DOI: 10.1002/adma.202308092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information-processing circuits into materials. Here, a set of protease-based biohybrid modules the bioactivity of which can either be induced or inhibited is engineered. Guided by a quantitative mathematical model and following a design-build-test-learn (DBTL) cycle, the modules are wired according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. A 2-input/4-output binary decoder for the detection of two small molecules in a material framework that can perform regulated outputs in form of distinct protease activities is designed. The here demonstrated smart material system is strongly modular and can be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.
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Affiliation(s)
- Hasti Mohsenin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Hanna J Wagner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104, Freiburg, Germany
| | - Marcus Rosenblatt
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Svenja Kemmer
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Pitter Huesgen
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Jens Timmer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104, Freiburg, Germany
- Saarland University, Department of Materials Science and Engineering, Campus D2 2, 66123, Saarbrücken, Germany
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Wagner HJ, Mohsenin H, Weber W. Synthetic Biology-Empowered Hydrogels for Medical Diagnostics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 178:197-226. [PMID: 33582837 DOI: 10.1007/10_2020_158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Synthetic biology is strongly inspired by concepts of engineering science and aims at the design and generation of artificial biological systems in different fields of research such as diagnostics, analytics, biomedicine, or chemistry. To this aim, synthetic biology uses an engineering approach relying on a toolbox of molecular sensors and switches that endows cellular hosts with non-natural computing functions and circuits. Importantly, this concept is not only limited to cellular approaches. Synthetic biological building blocks have also conferred sensing and switching capability to otherwise inactive materials. This principle has attracted high interest for the development of biohybrid materials capable of sensing and responding to specific molecular stimuli, such as disease biomarkers, antibiotics, or heavy metals. Moreover, the interconnection of individual sense-and-respond materials to complex materials systems has enabled the processing of, for example, multiple inputs or the amplification of signals using feedback topologies. Such systems holding high potential for applications in the analytical and diagnostic sectors will be described in this chapter.
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Affiliation(s)
- Hanna J Wagner
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Hasti Mohsenin
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wilfried Weber
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.
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Xu M, Hao X, Hu Z, Yan Q. Palladium-bridged polymers as CO-biosignal-responsive self-healing hydrogels. Polym Chem 2020. [DOI: 10.1039/c9py01660k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Using a CO biosignal to trigger the dissociation of Pd-bridged polymer hydrogel.
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Affiliation(s)
- Miaomiao Xu
- State Key Laboratory of Molecular Engineering of Polymers
- Fudan University
- Shanghai 200433
- China
| | - Xiang Hao
- State Key Laboratory of Molecular Engineering of Polymers
- Fudan University
- Shanghai 200433
- China
| | - Zhiwei Hu
- State Key Laboratory of Molecular Engineering of Polymers
- Fudan University
- Shanghai 200433
- China
| | - Qiang Yan
- State Key Laboratory of Molecular Engineering of Polymers
- Fudan University
- Shanghai 200433
- China
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Wagner HJ, Sprenger A, Rebmann B, Weber W. Upgrading biomaterials with synthetic biological modules for advanced medical applications. Adv Drug Deliv Rev 2016; 105:77-95. [PMID: 27179764 DOI: 10.1016/j.addr.2016.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/02/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
One key aspect of synthetic biology is the development and characterization of modular biological building blocks that can be assembled to construct integrated cell-based circuits performing computational functions. Likewise, the idea of extracting biological modules from the cellular context has led to the development of in vitro operating systems. This principle has attracted substantial interest to extend the repertoire of functional materials by connecting them with modules derived from synthetic biology. In this respect, synthetic biological switches and sensors, as well as biological targeting or structure modules, have been employed to upgrade functions of polymers and solid inorganic material. The resulting systems hold great promise for a variety of applications in diagnosis, tissue engineering, and drug delivery. This review reflects on the most recent developments and critically discusses challenges concerning in vivo functionality and tolerance that must be addressed to allow the future translation of such synthetic biology-upgraded materials from the bench to the bedside.
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Huang W, Tarakanova A, Dinjaski N, Wang Q, Xia X, Chen Y, Wong JY, Buehler MJ, Kaplan DL. Design of Multistimuli Responsive Hydrogels Using Integrated Modeling and Genetically Engineered Silk-Elastin-Like Proteins. ADVANCED FUNCTIONAL MATERIALS 2016; 26:4113-4123. [PMID: 28670244 PMCID: PMC5488272 DOI: 10.1002/adfm.201600236] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Elastomeric, robust, and biocompatible hydrogels are rare, while the need for these types of biomaterials in biomedical-related uses remains high. Here, a new family of genetically engineered silk-elastin copolymers (SELPs) with encoded enzymatic crosslinking sites is developed for a new generation of stimuli-responsive yet robust hydrogels. Input into the designs is guided by simulation, and realized via genetic engineering strategies. The avoidance of gamma irradiation or chemical crosslinking during gel fabrication, in lieu of an enzymatic process, expands the versatility of these new gels for the incorporation of labile proteins and cells. In the present study, the new SELP hydrogels offers sequence dependent, reversible stimuli-responsive features. Their stiffness covers almost the full range of the elasticity of soft tissues. Further, physical modification of the silk domains provided a secondary control point to fine-tune mechanical stiffness while preserving stimuli-responsive features, with implications for a variety of biomedical materials and device needs.
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Affiliation(s)
- Wenwen Huang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Anna Tarakanova
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nina Dinjaski
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Qin Wang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Xiaoxia Xia
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Ying Chen
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Joyce Y Wong
- Departments of Biomedical Engineering and Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
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Lim HL, Hwang Y, Kar M, Varghese S. Smart hydrogels as functional biomimetic systems. Biomater Sci 2014; 2:603-618. [DOI: 10.1039/c3bm60288e] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review discusses the principles underlying stimuli-responsive behavior of hydrogels and how these properties contribute to their biomimetic functions and applications.
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Affiliation(s)
- Han L. Lim
- Department of Bioengineering
- University of California
- La Jolla, USA
| | - Yongsung Hwang
- Department of Bioengineering
- University of California
- La Jolla, USA
| | - Mrityunjoy Kar
- Department of Bioengineering
- University of California
- La Jolla, USA
| | - Shyni Varghese
- Department of Bioengineering
- University of California
- La Jolla, USA
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Hotz N, Wilcke L, Weber W. Design, synthesis, and application of stimulus-sensing biohybrid hydrogels. Macromol Rapid Commun 2013; 34:1594-610. [PMID: 23982955 DOI: 10.1002/marc.201300468] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/22/2013] [Indexed: 12/18/2022]
Abstract
A key feature of any living system is the ability to sense and react to the environmental stimuli. The biochemical characterization of the underlying biological sensors combined with advances in polymer chemistry has enabled the development of stimulus-sensitive biohybrid materials that translate most diverse chemical and biological input into a precise change in material properties. In this review article, we first describe synthesis strategies of how biological and chemical polymers can functionally be interconnected. We then provide a comprehensive overview of how the different properties of biological sensor molecules such as competitive target binding and allosteric modulation can be harnessed to develop responsive materials with applications in tissue engineering and drug delivery.
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Affiliation(s)
- Natascha Hotz
- Faculty of Biology, BIOSS - Centre for Biological Signalling Studies, SGBM - Spemann Graduate School of Biology and Medicine, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
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Xiong X, Zhou C, Wu C, Zhu G, Chen Z, Tan W. Responsive DNA-based hydrogels and their applications. Macromol Rapid Commun 2013; 34:1271-83. [PMID: 23857726 PMCID: PMC4470902 DOI: 10.1002/marc.201300411] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/17/2013] [Indexed: 11/06/2022]
Abstract
The term hydrogel describes a type of soft and wet material formed by cross-linked hydrophilic polymers. The distinct feature of hydrogels is their ability to absorb a large amount of water and swell. The properties of a hydrogel are usually determined by the chemical properties of their constituent polymer(s). However, a group of hydrogels, called "smart hydrogels," changes properties in response to environmental changes or external stimuli. Recently, DNA or DNA-inspired responsive hydrogels have attracted considerable attention in construction of smart hydrogels because of the intrinsic advantages of DNA. As a biological polymer, DNA is hydrophilic, biocompatible, and highly programmable by Watson-Crick base pairing. DNA can form a hydrogel by itself under certain conditions, and it can also be incorporated into synthetic polymers to form DNA-hybrid hydrogels. Functional DNAs, such as aptamers and DNAzymes, provide additional molecular recognition capabilities and versatility. In this Review, DNA-based hydrogels are discussed in terms of their stimulus response, as well as their applications.
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Affiliation(s)
- Xiangling Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio- Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Cuisong Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio- Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Cuichen Wu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio- Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Guizhi Zhu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio- Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | | | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio- Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
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A biohybrid hydrogel for the urate-responsive release of urate oxidase. J Control Release 2013; 171:57-62. [PMID: 23838153 DOI: 10.1016/j.jconrel.2013.06.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/27/2013] [Accepted: 06/29/2013] [Indexed: 01/12/2023]
Abstract
Functional biomaterials that detect and correct pathological parameters hold high promises for biomedical application. In this study we describe a biohybrid hydrogel that detects elevated concentrations of uric acid and responds by dissolution and the release of uric acid-degrading urate oxidase. This material was synthesized by incorporating PEG-stabilized urate oxidase into a polyacrylamide hydrogel that was crosslinked by the uric acid-sensitive interaction between the uric acid transcription factor HucR and its operator hucO. We characterize the uric acid responsiveness of the material and demonstrate that it can effectively be applied to counteract flares of uric acid in a mouse model. This approach might be a first step towards a biomedical device autonomously managing uric acid burst associated to gouty arthritis and the tumor lysis syndrome.
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