1
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Rubanov M, Cole J, Lee HJ, Soto Cordova LG, Chen Z, Gonzalez E, Schulman R. Multi-domain automated patterning of DNA-functionalized hydrogels. PLoS One 2024; 19:e0295923. [PMID: 38306330 PMCID: PMC10836684 DOI: 10.1371/journal.pone.0295923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/04/2023] [Indexed: 02/04/2024] Open
Abstract
DNA-functionalized hydrogels are capable of sensing oligonucleotides, proteins, and small molecules, and specific DNA sequences sensed in the hydrogels' environment can induce changes in these hydrogels' shape and fluorescence. Fabricating DNA-functionalized hydrogel architectures with multiple domains could make it possible to sense multiple molecules and undergo more complicated macroscopic changes, such as changing fluorescence or changing the shapes of regions of the hydrogel architecture. However, automatically fabricating multi-domain DNA-functionalized hydrogel architectures, capable of enabling the construction of hydrogel architectures with tens to hundreds of different domains, presents a significant challenge. We describe a platform for fabricating multi-domain DNA-functionalized hydrogels automatically at the micron scale, where reaction and diffusion processes can be coupled to program material behavior. Using this platform, the hydrogels' material properties, such as shape and fluorescence, can be programmed, and the fabricated hydrogels can sense their environment. DNA-functionalized hydrogel architectures with domain sizes as small as 10 microns and with up to 4 different types of domains can be automatically fabricated using ink volumes as low as 50 μL. We also demonstrate that hydrogels fabricated using this platform exhibit responses similar to those of DNA-functionalized hydrogels fabricated using other methods by demonstrating that DNA sequences can hybridize within them and that they can undergo DNA sequence-induced shape change.
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Affiliation(s)
- Moshe Rubanov
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Joshua Cole
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Heon-Joon Lee
- Department of Biomedical Engineering, Whiting School of Engineering and the School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Leandro G. Soto Cordova
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Zachary Chen
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Elia Gonzalez
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
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2
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Nam H, Kim T, Moon S, Ji Y, Lee JB. Self-assembly of a multimeric genomic hydrogel via multi-primed chain reaction of dual single-stranded circular plasmids for cell-free protein production. iScience 2023; 26:107089. [PMID: 37416467 PMCID: PMC10319821 DOI: 10.1016/j.isci.2023.107089] [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: 01/27/2023] [Revised: 04/20/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
Recent technical advances in cell-free protein synthesis (CFPS) offer several advantages over cell-based expression systems, including the application of cellular machinery, such as transcription and translation, in the test tube. Inspired by the advantages of CFPS, we have fabricated a multimeric genomic DNA hydrogel (mGD-gel) via rolling circle chain amplification (RCCA) using dual single-stranded circular plasmids with multiple primers. The mGD-gel exhibited significantly enhanced protein yield. In addition, mGD-gel can be reused at least five times, and the shape of the mGD-gel can be easily manipulated without losing the feasibility of protein expression. The mGD-gel platform based on the self-assembly of multimeric genomic DNA strands (mGD strands) has the potential to be used in CFPS systems for a variety of biotechnological applications.
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Affiliation(s)
- Hyangsu Nam
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Taehyeon Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Sunghyun Moon
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
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3
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Zhang D, Li L, Fang Y, Ma Q, Cao Y, Lei H. Ester Bonds for Modulation of the Mechanical Properties of Protein Hydrogels. Int J Mol Sci 2023; 24:10778. [PMID: 37445957 DOI: 10.3390/ijms241310778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Hydrogels are soft materials constructed of physically or chemically crosslinked polymeric net-works with abundant water. The crosslinkers, as the mechanophores that bear and respond to mechanical forces, play a critical role in determining the mechanical properties of hydrogels. Here, we use a polyprotein as the crosslinker and mechanophore to form covalent polymer hydrogels in which the toughness and fatigue fracture are controlled by the mechanical unfolding of polyproteins. The protein Parvimonas sp. (ParV) is super stable and remains folded even at forces > 2 nN; however, it can unfold under loading forces of ~100 pN at basic pH values or low calcium concentrations due to destabilization of the protein structures. Through tuning the protein unfolding by pH and calcium concentrations, the hydrogel exhibits differences in modulus, strength, and anti-fatigue fracture. We found that due to the partially unfolding of ParV, the Young's modulus decreased at pH 9.0 or in the presence of EDTA (Ethylene Diamine Tetraacetic Acid), moreover, because partially unfolded ParV can be further completely unfolded due to the mechanically rupture of ester bond, leading to the observed hysteresis of the stretching and relaxation traces of the hydrogels, which is in line with single-molecule force spectroscopy experiments. These results display a new avenue for designing pH- or calcium-responsive hydrogels based on proteins and demonstrate the relationship between the mechanical properties of single molecules and macroscopic hydrogel networks.
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Affiliation(s)
- Di Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Luofei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Yizhou Fang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Quan Ma
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing 210093, China
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4
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Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023; 7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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5
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Wu H, Zheng B. Hydrogel-Based Multi-enzymatic System for Biosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:51-76. [PMID: 37306702 DOI: 10.1007/10_2023_220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biosynthesis involving multi-enzymatic reactions is usually an efficient and economic method to produce plentiful important molecules. To increase the product yield in biosynthesis, the involved enzymes can be immobilized to carriers for enhancing enzyme stability, increasing synthesis efficiency and improving enzyme recyclability. Hydrogels with three-dimensional porous structures and versatile functional groups are promising carriers for enzyme immobilization. Herein, we review the recent advances of the hydrogel-based multi-enzymatic system for biosynthesis. First, we introduce the strategies of enzyme immobilization in hydrogel, including the pros and cons of the strategies. Then we overview the recent applications of the multi-enzymatic system for biosynthesis, including cell-free protein synthesis (CFPS) and non-protein synthesis, especially high value-added molecules. In the last section, we discuss the future perspective of the hydrogel-based multi-enzymatic system for biosynthesis.
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Affiliation(s)
- Han Wu
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Bo Zheng
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
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6
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Sánchez-Costa M, López-Gallego F. Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:21-46. [PMID: 37306703 DOI: 10.1007/10_2023_226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.
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Affiliation(s)
- Mercedes Sánchez-Costa
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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7
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Li DY, Zhou ZH, Yu YL, Deng NN. Microfluidic construction of cytoskeleton-like hydrogel matrix for stabilizing artificial cells. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Abstract
Recent years have seen substantial efforts aimed at constructing artificial cells from various molecular components with the aim of mimicking the processes, behaviours and architectures found in biological systems. Artificial cell development ultimately aims to produce model constructs that progress our understanding of biology, as well as forming the basis for functional bio-inspired devices that can be used in fields such as therapeutic delivery, biosensing, cell therapy and bioremediation. Typically, artificial cells rely on a bilayer membrane chassis and have fluid aqueous interiors to mimic biological cells. However, a desire to more accurately replicate the gel-like properties of intracellular and extracellular biological environments has driven increasing efforts to build cell mimics based on hydrogels. This has enabled researchers to exploit some of the unique functional properties of hydrogels that have seen them deployed in fields such as tissue engineering, biomaterials and drug delivery. In this Review, we explore how hydrogels can be leveraged in the context of artificial cell development. We also discuss how hydrogels can potentially be incorporated within the next generation of artificial cells to engineer improved biological mimics and functional microsystems.
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9
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Budharaju H, Zennifer A, Sethuraman S, Paul A, Sundaramurthi D. Designer DNA biomolecules as a defined biomaterial for 3D bioprinting applications. MATERIALS HORIZONS 2022; 9:1141-1166. [PMID: 35006214 DOI: 10.1039/d1mh01632f] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA has excellent features such as the presence of functional and targeted molecular recognition motifs, tailorability, multifunctionality, high-precision molecular self-assembly, hydrophilicity, and outstanding biocompatibility. Due to these remarkable features, DNA has emerged as a leading next-generation biomaterial of choice to make hydrogels by self-assembly. In recent times, novel routes for the chemical synthesis of DNA, advances in tailorable designs, and affordable production ways have made DNA as a building block material for various applications. These advanced features have made researchers continuously explore the interesting properties of pure and hybrid DNA for 3D bioprinting and other biomedical applications. This review article highlights the topical advancements in the use of DNA as an ideal bioink for the bioprinting of cell-laden three-dimensional tissue constructs for regenerative medicine applications. Various bioprinting techniques and emerging design approaches such as self-assembly, nucleotide sequence, enzymes, and production cost to use DNA as a bioink for bioprinting applications are described. In addition, various types and properties of DNA hydrogels such as stimuli responsiveness and mechanical properties are discussed. Further, recent progress in the applications of DNA in 3D bioprinting are emphasized. Finally, the current challenges and future perspectives of DNA hydrogels in 3D bioprinting and other biomedical applications are discussed.
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Affiliation(s)
- Harshavardhan Budharaju
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
| | - Allen Zennifer
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
| | - Swaminathan Sethuraman
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Dhakshinamoorthy Sundaramurthi
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
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10
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Fabrini G, Minard A, Brady RA, Di Antonio M, Di Michele L. Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures. NANO LETTERS 2022; 22:602-611. [PMID: 35026112 PMCID: PMC8796241 DOI: 10.1021/acs.nanolett.1c03314] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.
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Affiliation(s)
- Giacomo Fabrini
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Aisling Minard
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Ryan A. Brady
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Marco Di Antonio
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Lorenzo Di Michele
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
- Department
of Physics—Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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11
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Beabout K, Bernhards CB, Thakur M, Turner KB, Cole SD, Walper SA, Chávez JL, Lux MW. Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems. ACS Synth Biol 2021; 10:3040-3054. [PMID: 34723503 DOI: 10.1021/acssynbio.1c00331] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Many bacterial mechanisms for highly specific and sensitive detection of heavy metals and other hazards have been reengineered to serve as sensors. In some cases, these sensors have been implemented in cell-free expression systems, enabling easier design optimization and deployment in low-resource settings through lyophilization. Here, we apply the advantages of cell-free expression systems to optimize sensors based on three separate bacterial response mechanisms for arsenic, cadmium, and mercury. We achieved detection limits below the World Health Organization-recommended levels for arsenic and mercury and below the short-term US Military Exposure Guideline levels for all three. The optimization of each sensor was approached differently, leading to observations useful for the development of future sensors: (1) there can be a strong dependence of specificity on the particular cell-free expression system used, (2) tuning of relative concentrations of the sensing and reporter elements improves sensitivity, and (3) sensor performance can vary significantly with linear vs plasmid DNA. In addition, we show that simply combining DNA for the three sensors into a single reaction enables detection of each target heavy metal without any further optimization. This combined approach could lead to sensors that detect a range of hazards at once, such as a panel of water contaminants or all known variants of a target virus. For low-resource settings, such "all-hazard" sensors in a cheap, easy-to-use format could have high utility.
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Affiliation(s)
- Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Casey B. Bernhards
- Excet, Inc., 6225 Brandon Avenue #360, Springfield, Virginia 22150, United States
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Meghna Thakur
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kendrick B. Turner
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Stephanie D. Cole
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Jorge L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Matthew W. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
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12
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DNA mediated graphene oxide (GO)-nanosheets dispersed supramolecular GO-DNA hydrogel: An efficient soft-milieu for simplistic synthesis of Ag-NPs@GO-DNA and Gram + ve/-ve bacteria-based Ag-NPs@GO-DNA-bacteria nano-bio composites. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Vezeau GE, Salis HM. Tuning Cell-Free Composition Controls the Time Delay, Dynamics, and Productivity of TX-TL Expression. ACS Synth Biol 2021; 10:2508-2519. [PMID: 34498860 DOI: 10.1021/acssynbio.1c00136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The composition of cell-free expression systems (TX-TL) is adjusted by adding macromolecular crowding agents and salts. However, the effects of these cosolutes on the dynamics of individual gene expression processes have not been quantified. Here, we carry out kinetic mRNA and protein level measurements on libraries of genetic constructs using the common cosolutes PEG-8000, Ficoll-400, and magnesium glutamate. By combining these measurements with biophysical modeling, we show that cosolutes have differing effects on transcription initiation, translation initiation, and translation elongation rates with trade-offs between time delays, expression tunability, and maximum expression productivity. We also confirm that biophysical models can predict translation initiation rates in TX-TL using Escherichia coli lysate. We discuss how cosolute composition can be tuned to maximize performance across different cell-free applications, including biosensing, diagnostics, and biomanufacturing.
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Affiliation(s)
- Grace E. Vezeau
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Howard M. Salis
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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14
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Formulation of DNA Nanocomposites: Towards Functional Materials for Protein Expression. Polymers (Basel) 2021; 13:polym13152395. [PMID: 34371999 PMCID: PMC8347857 DOI: 10.3390/polym13152395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
DNA hydrogels are an emerging class of materials that hold great promise for numerous biotechnological applications, ranging from tissue engineering to targeted drug delivery and cell-free protein synthesis (CFPS). In addition to the molecular programmability of DNA that can be used to instruct biological systems, the formulation of DNA materials, e.g., as bulk hydrogels or microgels, is also relevant for specific applications. To advance the state of knowledge in this research area, the present work explores the scope of a recently developed class of complex DNA nanocomposites, synthesized by RCA polymerization of DNA-functionalized silica nanoparticles (SiNPs) and carbon nanotubes (CNTs). SiNP/CNT-DNA composites were produced as bulk materials and microgels which contained a plasmid with transcribable genetic information for a fluorescent marker protein. Using confocal microscopy and flow cytometry, we found that the materials are very efficiently taken up by various eukaryotic cell lines, which were able to continue dividing while the ingested material was evenly distributed to the daughter cells. However, no expression of the encoded protein occurred within the cells. While the microgels did not induce production of the marker protein even in a CFPS procedure with eukaryotic cell lysate, the bulk composites proved to be efficient templates for CFPS. This work contributes to the understanding of the molecular interactions between DNA composites and the functional cellular machinery. Implications for the use of such materials for CFPS procedures are discussed.
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15
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Jian X, Feng X, Luo Y, Li F, Tan J, Yin Y, Liu Y. Development, Preparation, and Biomedical Applications of DNA-Based Hydrogels. Front Bioeng Biotechnol 2021; 9:661409. [PMID: 34150729 PMCID: PMC8206814 DOI: 10.3389/fbioe.2021.661409] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/20/2021] [Indexed: 12/31/2022] Open
Abstract
Hydrogels have outstanding research and application prospects in the biomedical field. Among them, the design and preparation of biomedical hydrogels with deoxyribonucleic acid (DNA) as building blocks have attracted increasing research interest. DNA-based hydrogel not only has the skeleton function of hydrogel, but also retains its biological functions, including its excellent selection specificity, structural designability, precise molecular recognition ability, outstanding biocompatibility, and so on. It has shown important application prospects in the biomedical field, such as drug delivery, biosensing, and tissue engineering. In recent years, researchers have made full use of the characteristics of DNA molecules and constructed various pure DNA-based hydrogels with excellent properties through various crosslinking methods. Moreover, via introducing functional molecules or elements, or combining with other functional materials, a variety of multifunctional DNA-based hybrid hydrogels have also been constructed, which expand the breadth and depth of their applications. Here, we described the recent development trend in the area of DNA-based hydrogels and highlighted various preparation methods of DNA-based hydrogels. Representative biomedical applications are also exemplified to show the high performance of DNA-based hydrogels. Meanwhile, the existing problems and prospects are also summarized. This review provided references for the further development of DNA-based hydrogels.
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Affiliation(s)
| | | | | | | | | | | | - Yang Liu
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, University of South China, Hengyang, China
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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Blum SM, Lee MS, Mgboji GE, Funk VL, Beabout K, Harbaugh SV, Roth PA, Liem AT, Miklos AE, Emanuel PA, Walper SA, Chávez JL, Lux MW. Impact of Porous Matrices and Concentration by Lyophilization on Cell-Free Expression. ACS Synth Biol 2021; 10:1116-1131. [PMID: 33843211 DOI: 10.1021/acssynbio.0c00634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cell-free expression systems have drawn increasing attention as a tool to achieve complex biological functions outside of the cell. Several applications of the technology involve the delivery of functionality to challenging environments, such as field-forward diagnostics or point-of-need manufacturing of pharmaceuticals. To achieve these goals, cell-free reaction components are preserved using encapsulation or lyophilization methods, both of which often involve an embedding of components in porous matrices like paper or hydrogels. Previous work has shown a range of impacts of porous materials on cell-free expression reactions. Here, we explored a panel of 32 paperlike materials and 5 hydrogel materials for the impact on reaction performance. The screen included a tolerance to lyophilization for reaction systems based on both cell lysates and purified expression components. For paperlike materials, we found that (1) materials based on synthetic polymers were mostly incompatible with cell-free expression, (2) lysate-based reactions were largely insensitive to the matrix for cellulosic and microfiber materials, and (3) purified systems had an improved performance when lyophilized in cellulosic but not microfiber matrices. The impact of hydrogel materials ranged from completely inhibitory to a slight enhancement. The exploration of modulating the rehydration volume of lyophilized reactions yielded reaction speed increases using an enzymatic colorimetric reporter of up to twofold with an optimal ratio of 2:1 lyophilized reaction to rehydration volume for the lysate system and 1.5:1 for the purified system. The effect was independent of the matrices assessed. Testing with a fluorescent nonenzymatic reporter and no matrix showed similar improvements in both yields and reaction speeds for the lysate system and yields but not reaction speeds for the purified system. We finally used these observations to show an improved performance of two sensors that span reaction types, matrix, and reporters. In total, these results should enhance efforts to develop field-forward applications of cell-free expression systems.
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Affiliation(s)
- Steven M. Blum
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Marilyn S. Lee
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Glory E. Mgboji
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37830-6209, United States
| | - Vanessa L. Funk
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Svetlana V. Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Pierce A. Roth
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- DCS Corporation, 4696 Millenium Drive, Suite 450, Belcamp, Maryland 21017, United States
| | - Alvin T. Liem
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
- DCS Corporation, 4696 Millenium Drive, Suite 450, Belcamp, Maryland 21017, United States
| | - Aleksandr E. Miklos
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Peter A. Emanuel
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Jorge Luis Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Matthew W. Lux
- United States Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Aberdeen, Maryland 21010, United States
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Abstract
Supramolecular biopolymers (SBPs) are those polymeric units derived from macromolecules that can assemble with each other by noncovalent interactions. Macromolecular structures are commonly found in living systems such as proteins, DNA/RNA, and polysaccharides. Bioorganic chemistry allows the generation of sequence-specific supramolecular units like SBPs that can be tailored for novel applications in tissue engineering (TE). SBPs hold advantages over other conventional polymers previously used for TE; these materials can be easily functionalized; they are self-healing, biodegradable, stimuli-responsive, and nonimmunogenic. These characteristics are vital for the further development of current trends in TE, such as the use of pluripotent cells for organoid generation, cell-free scaffolds for tissue regeneration, patient-derived organ models, and controlled delivery systems of small molecules. In this review, we will analyse the 3 subtypes of SBPs: peptide-, nucleic acid-, and oligosaccharide-derived. Then, we will discuss the role that SBPs will be playing in TE as dynamic scaffolds, therapeutic scaffolds, and bioinks. Finally, we will describe possible outlooks of SBPs for TE.
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Benítez-Mateos AI, Zeballos N, Comino N, Moreno de Redrojo L, Randelovic T, López-Gallego F. Microcompartmentalized Cell-Free Protein Synthesis in Hydrogel μ-Channels. ACS Synth Biol 2020; 9:2971-2978. [PMID: 33170665 DOI: 10.1021/acssynbio.0c00462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rapid demand for protein-based molecules has stimulated much research on cell-free protein synthesis (CFPS); however, there are still many challenges in terms of cost-efficiency, process intensification, and sustainability. Herein, we describe the microcompartmentalization of CFPS of superfolded green fluorescent protein (sGFP) in alginate hydrogels, which were casted into a μ-channel device. CFPS was optimized for the microcompartmentalized environment and characterized in terms of synthesis yield. To extend the scope of this technology, the use of other biocompatible materials (collagen, laponite, and agarose) was explored. In addition, the diffusion of sGFP from the hydrogel microenvironment to the bulk was demonstrated, opening a promising opportunity for concurrent synthesis and delivery of proteins. Finally, we provide an application for this system: the CFPS of enzymes. The present design of the hydrogel μ-channel device may enhance the potential application of microcompartmentalized CFPS in biosensing, bioprototyping, and therapeutic development.
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Affiliation(s)
- Ana I. Benítez-Mateos
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
- Heterogeneous Biocatalysis Laboratory, Instituto de Síntesis Química y Catálisis Homogénea (iSQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Nicoll Zeballos
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
| | - Natalia Comino
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
| | - Lucía Moreno de Redrojo
- Heterogeneous Biocatalysis Laboratory, Instituto de Síntesis Química y Catálisis Homogénea (iSQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Teodora Randelovic
- Tissue MicroEnvironment (TME) Lab, Institute for Health Research Aragón (IISA), Avda. San Juan Bosco 13, 50009 Zaragoza, Spain
- Aragon Institute of Engineering Research (I3A), University of Zaragoza, Mariano Escuillor s/n, 50018 Zaragoza, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, CICbiomaGUNE, Paseo Miramón 182. Edificio empresarial “C”, 20014 San Sebastián, Spain
- Heterogeneous Biocatalysis Laboratory, Instituto de Síntesis Química y Catálisis Homogénea (iSQCH), CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- ARAID, Aragon Foundation for Science, 50009 Zaragoza, Spain
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Morya V, Walia S, Mandal BB, Ghoroi C, Bhatia D. Functional DNA Based Hydrogels: Development, Properties and Biological Applications. ACS Biomater Sci Eng 2020; 6:6021-6035. [DOI: 10.1021/acsbiomaterials.0c01125] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Vinod Morya
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Shanka Walia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Biman B Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam India
| | - Chinmay Ghoroi
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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21
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Lee MS, Hung CS, Phillips DA, Buck CC, Gupta MK, Lux MW. Silk fibroin as an additive for cell-free protein synthesis. Synth Syst Biotechnol 2020; 5:145-154. [PMID: 32637668 PMCID: PMC7320238 DOI: 10.1016/j.synbio.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023] Open
Abstract
Cell-free systems contain many proteins and metabolites required for complex functions such as transcription and translation or multi-step metabolic conversions. Research into expanding the delivery of these systems by drying or by embedding into other materials is enabling new applications in sensing, point-of-need manufacturing, and responsive materials. Meanwhile, silk fibroin from the silk worm, Bombyx mori, has received attention as a protective additive for dried enzyme formulations and as a material to build biocompatible hydrogels for controlled localization or delivery of biomolecular cargoes. In this work, we explore the effects of silk fibroin as an additive in cell-free protein synthesis (CFPS) reactions. Impacts of silk fibroin on CFPS activity and stability after drying, as well as the potential for incorporation of CFPS into hydrogels of crosslinked silk fibroin are assessed. We find that simple addition of silk fibroin increased productivity of the CFPS reactions by up to 42%, which we attribute to macromolecular crowding effects. However, we did not find evidence that silk fibroin provides a protective effects after drying as previously described for purified enzymes. Further, the enzymatic crosslinking transformations of silk fibroin typically used to form hydrogels are inhibited in the presence of the CFPS reaction mixture. Crosslinking attempts did not impact CFPS activity, but did yield localized protein aggregates rather than a hydrogel. We discuss the mechanisms at play in these results and how the silk fibroin-CFPS system might be improved for the design of cell-free devices.
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Affiliation(s)
- Marilyn S. Lee
- US Army Combat Capabilities Development Command Chemical and Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Chia-Suei Hung
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
| | - Daniel A. Phillips
- US Naval Research Laboratory Center for Bio/Molecular Science and Engineering, Bldg. 42, Room 303 4555 Overlook Ave. Washington, DC 20375, UES Inc., 4401 Dayton Xenia Rd., Beavercreek, OH 45432, USA
| | - Chelsea C. Buck
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
- US Naval Research Laboratory Center for Bio/Molecular Science and Engineering, Bldg. 42, Room 303 4555 Overlook Ave. Washington, DC 20375, UES Inc., 4401 Dayton Xenia Rd., Beavercreek, OH 45432, USA
| | - Maneesh K. Gupta
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical and Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
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