1
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Lin S, Riaud A, Zhou J. Selective Sparse Sampling of Water Droplets in Oil with Acoustic Tweezers. ACS Sens 2024; 9:2066-2074. [PMID: 38627252 DOI: 10.1021/acssensors.4c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2024]
Abstract
In microfluidics, water droplets are often used as independent biochemical microreactor units, enabling the implementation of massively parallel screening assays where only a few of the reacting water droplets yield a positive result. However, sampling the product of these few successful reactions is an unsolved challenge. One possible solution is to use acoustic tweezers, which are lab-free, easily miniaturized, and biocompatible manipulation tools, and existing acoustic tweezers manipulating particles or cells, and water droplet manipulation in oil with an acoustic tweezer is absent. The first challenge in attempting to recover a few water droplets from a large batch is the selective manipulation of water droplets in an oil system. In this paper, we trap and manipulate single water droplets in oil using integrated single-beam (focused beam/vortex beam) acoustic tweezers for the first time. We find that water droplets with a diameter smaller than half a wavelength are trapped by acoustic vortices, while larger ones are better captured by focused acoustic beams. It is the first step to extract the target water droplet microreactors (positive ones) in an oil system and analyze their content. Compared to previous techniques, such as fluorescence-activated cell sorting (FACS), our technique is sparse, meaning that the sampling time is proportional to the number of droplets required and very insensitive to the total number of microreactors, making it well suited for large-scale screening assays.
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Affiliation(s)
- Siying Lin
- School of Microelectronics, Fudan University, Shanghai 200433, China
| | - Antoine Riaud
- School of Microelectronics, Fudan University, Shanghai 200433, China
| | - Jia Zhou
- School of Microelectronics, Fudan University, Shanghai 200433, China
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2
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Yang Y, Vagin SI, Rieger B, Destgeer G. Fabrication of Crescent Shaped Microparticles for Particle Templated Droplet Formation. Macromol Rapid Commun 2024:e2300721. [PMID: 38615246 DOI: 10.1002/marc.202300721] [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: 12/12/2023] [Revised: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Crescent-shaped hydrogel microparticles are shown to template uniform volume aqueous droplets upon simple mixing with aqueous and oil media for various bioassays. This emerging "lab on a particle" technique requires hydrogel particles with tunable material properties and dimensions. The crescent shape of the particles is attained by aqueous two-phase separation of polymers followed by photopolymerization of the curable precursor. In this work, the phase separation of poly(ethylene glycol) diacrylate (PEGDA, Mw 700) and dextran (Mw 40 000) for tunable manufacturing of crescent-shaped particles is investigated. The particles' morphology is precisely tuned by following a phase diagram, varying the UV intensity, and adjusting the flow rates of various streams. The fabricated particles with variable dimensions encapsulate uniform aqueous droplets upon mixing with an oil phase. The particles are fluorescently labeled with red and blue emitting dyes at variable concentrations to produce six color-coded particles. The blue fluorescent dye shows a moderate response to the pH change. The fluorescently labeled particles are able to tolerate an extremely acidic solution (pH 1) but disintegrate within an extremely basic solution (pH 14). The particle-templated droplets are able to effectively retain the disintegrating particle and the fluorescent signal at pH 14.
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Affiliation(s)
- Yimin Yang
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
| | - Sergei I Vagin
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Bernhard Rieger
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Ghulam Destgeer
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
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3
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Enders A, Grünberger A, Bahnemann J. Towards Small Scale: Overview and Applications of Microfluidics in Biotechnology. Mol Biotechnol 2024; 66:365-377. [PMID: 36515858 PMCID: PMC10881759 DOI: 10.1007/s12033-022-00626-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022]
Abstract
Thanks to recent and continuing technological innovations, modern microfluidic systems are increasingly offering researchers working across all fields of biotechnology exciting new possibilities (especially with respect to facilitating high throughput analysis, portability, and parallelization). The advantages offered by microfluidic devices-namely, the substantially lowered chemical and sample consumption they require, the increased energy and mass transfer they offer, and their comparatively small size-can potentially be leveraged in every sub-field of biotechnology. However, to date, most of the reported devices have been deployed in furtherance of healthcare, pharmaceutical, and/or industrial applications. In this review, we consider examples of microfluidic and miniaturized systems across biotechnology sub-fields. In this context, we point out the advantages of microfluidics for various applications and highlight the common features of devices and the potential for transferability to other application areas. This will provide incentives for increased collaboration between researchers from different disciplines in the field of biotechnology.
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Affiliation(s)
- Anton Enders
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Alexander Grünberger
- Institute of Process Engineering in Life Sciences: Microsystems in Bioprocess Engineering, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131, Karlsruhe, Germany
| | - Janina Bahnemann
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159, Augsburg, Germany.
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4
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Strutt R, Xiong B, Abegg VF, Dittrich PS. Open microfluidics: droplet microarrays as next generation multiwell plates for high throughput screening. LAB ON A CHIP 2024; 24:1064-1075. [PMID: 38356285 PMCID: PMC10898417 DOI: 10.1039/d3lc01024d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
Multiwell plates are prominent in the biological and chemical sciences; however, they face limitations in terms of throughput and deployment in emerging bioengineering fields. Droplet microarrays, as an open microfluidic technology, organise tiny droplets typically in the order of thousands, on an accessible plate. In this perspective, we summarise current approaches for generating droplets, fluid handling on them, and analysis within droplet microarrays. By enabling unique plate engineering opportunities, demonstrating the necessary experimental procedures required for manipulating and interacting with biological cells, and integrating with label-free analytical techniques, droplet microarrays can be deployed across a more extensive experimental domain than what is currently covered by multiwell plates. Droplet microarrays thus offer a solution to the bottlenecks associated with multiwell plates, particularly in the areas of biological cultivation and high-throughput compound screening.
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Affiliation(s)
- Robert Strutt
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Bijing Xiong
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Vanessa Fabienne Abegg
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
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5
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Cheng G, Kuan CY, Lou KW, Ho YP. Light-Responsive Materials in Droplet Manipulation for Biochemical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2313935. [PMID: 38379512 DOI: 10.1002/adma.202313935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/31/2024] [Indexed: 02/22/2024]
Abstract
Miniaturized droplets, characterized by well-controlled microenvironments and capability for parallel processing, have significantly advanced the studies on enzymatic evolution, molecular diagnostics, and single-cell analysis. However, manipulation of small-sized droplets, including moving, merging, and trapping of the targeted droplets for complex biochemical assays and subsequent analysis, is not trivial and remains technically demanding. Among various techniques, light-driven methods stand out as a promising candidate for droplet manipulation in a facile and flexible manner, given the features of contactless interaction, high spatiotemporal resolution, and biocompatibility. This review therefore compiles an in-depth discussion of the governing mechanisms underpinning light-driven droplet manipulation. Besides, light-responsive materials, representing the core of light-matter interaction and the key character converting light into different forms of energy, are particularly assessed in this review. Recent advancements in light-responsive materials and the most notable applications are comprehensively archived and evaluated. Continuous innovations and rational engineering of light-responsive materials are expected to propel the development of light-driven droplet manipulation, equip droplets with enhanced functionality, and broaden the applications of droplets for biochemical studies and routine biochemical investigations.
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Affiliation(s)
- Guangyao Cheng
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Chit Yau Kuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Kuan Wen Lou
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, 999077, China
- Centre for Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
- The Ministry of Education Key Laboratory of Regeneration Medicine, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
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6
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Li X, Tang S, Zhang Y, Zhu J, Forgham H, Zhao C, Zhang C, Davis TP, Qiao R. Tailored Fluorosurfactants through Controlled/Living Radical Polymerization for Highly Stable Microfluidic Droplet Generation. Angew Chem Int Ed Engl 2024; 63:e202315552. [PMID: 38038248 PMCID: PMC10952479 DOI: 10.1002/anie.202315552] [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: 10/16/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/02/2023]
Abstract
Droplet-based microfluidics represents a disruptive technology in the field of chemistry and biology through the generation and manipulation of sub-microlitre droplets. To avoid droplet coalescence, fluoropolymer-based surfactants are commonly used to reduce the interfacial tension between two immiscible phases to stabilize droplet interfaces. However, the conventional preparation of fluorosurfactants involves multiple steps of conjugation reactions between fluorinated and hydrophilic segments to form multiple-block copolymers. In addition, synthesis of customized surfactants with tailored properties is challenging due to the complex synthesis process. Here, we report a highly efficient synthetic method that utilizes living radical polymerization (LRP) to produce fluorosurfactants with tailored functionalities. Compared to the commercialized surfactant, our surfactants outperform in thermal cycling for polymerase chain reaction (PCR) testing, and exhibit exceptional biocompatibility for cell and yeast culturing in a double-emulsion system. This breakthrough synthetic approach has the potential to revolutionize the field of droplet-based microfluidics by enabling the development of novel designs that generate droplets with superior stability and functionality for a wide range of applications.
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Affiliation(s)
- Xiangke Li
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Shi‐Yang Tang
- School of Electronics and Computer ScienceUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Yang Zhang
- School of Engineering, Faculty of Science and EngineeringMacquarie UniversitySydney, NSW2109Australia
| | - Jiayuan Zhu
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Helen Forgham
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Chun‐Xia Zhao
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
- School of Chemical Engineering and Advanced MaterialsThe University of AdelaideAdelaide, SA5005Australia
| | - Cheng Zhang
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Thomas P. Davis
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
| | - Ruirui Qiao
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandBrisbane, Queensland4072Australia
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7
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Pourmasoumi F, Hengoju S, Beck K, Stephan P, Klopfleisch L, Hoernke M, Rosenbaum MA, Kries H. Analysing Megasynthetase Mutants at High Throughput Using Droplet Microfluidics. Chembiochem 2023; 24:e202300680. [PMID: 37804133 DOI: 10.1002/cbic.202300680] [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: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases internal stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.
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Affiliation(s)
- Farzaneh Pourmasoumi
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Katharina Beck
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lukas Klopfleisch
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Hoernke
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
- Faculty of Chemistry, Martin-Luther-Universität, Von-Danckelmann-Platz 4, 06108, Halle (S.), Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstrasse 30, 95440, Bayreuth, Germany
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8
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Makey DM, Diehl RC, Xin Y, Murray BE, Stoll DR, Ruotolo BT, Grinias JP, Narayan ARH, Lopez-Carillo V, Stark M, Johnen P, Kennedy RT. High-Throughput Liquid Chromatographic Analysis Using a Segmented Flow Injector with a 1 s Cycle Time. Anal Chem 2023; 95:17028-17036. [PMID: 37943345 PMCID: PMC11027085 DOI: 10.1021/acs.analchem.3c03719] [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] [Indexed: 11/10/2023]
Abstract
High-throughput screening (HTS) workflows are revolutionizing many fields, including drug discovery, reaction discovery and optimization, diagnostics, sensing, and enzyme engineering. Liquid chromatography (LC) is commonly deployed during HTS to reduce matrix effects, distinguish isomers, and preconcentrate prior to detection, but LC separation time often limits throughput. Although subsecond LC separations have been demonstrated, they are rarely utilized during HTS due to limitations associated with the speed of common autosamplers. In this work, these limits are overcome by utilizing droplet microfluidics for sample introduction. In the method, a train of samples segmented by air are continuously pumped into the inlet of an LC injection valve that is actuated once each sample fills the sample loop. Coupled with 2.1 mm diameter × 5 mm long columns packed with 2.7 μm superficially porous C18 particles operated at 5 mL/min, the injector enabled separation of 3 components at 1 s/sample and analysis of a 96-well plate in 1.6 min with <2% peak area relative standard deviation. Analyte-dependent carryover was minimized by including wash droplets composed of organic solvent in between sample droplets. High-throughput LC coupled with mass spectrometric detection using the segmented flow injector was applied to a screen of inhibitors of a cytochrome P450-catalyzed hydroxylation reaction. Measurements of the reaction substrate and product concentrations made using fast LC with the segmented flow injector correlated well with measurements made using a more conventional, 3 min LC method. These results demonstrate the potential for droplet microfluidics to be used for sample introduction during high-throughput LC analysis.
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Affiliation(s)
- Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Roger C Diehl
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yue Xin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bridget E Murray
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dwight R Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, Minnesota 56082, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Michailidou F. Engineering of Therapeutic and Detoxifying Enzymes. Angew Chem Int Ed Engl 2023; 62:e202308814. [PMID: 37433049 DOI: 10.1002/anie.202308814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/13/2023]
Abstract
Therapeutic enzymes present excellent opportunities for the treatment of human disease, modulation of metabolic pathways and system detoxification. However, current use of enzyme therapy in the clinic is limited as naturally occurring enzymes are seldom optimal for such applications and require substantial improvement by protein engineering. Engineering strategies such as design and directed evolution that have been successfully implemented for industrial biocatalysis can significantly advance the field of therapeutic enzymes, leading to biocatalysts with new-to-nature therapeutic activities, high selectivity, and suitability for medical applications. This minireview highlights case studies of how state-of-the-art and emerging methods in protein engineering are explored for the generation of therapeutic enzymes and discusses gaps and future opportunities in the field of enzyme therapy.
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Affiliation(s)
- Freideriki Michailidou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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10
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Li Z, Deng Y, Yang GY. Growth-coupled high throughput selection for directed enzyme evolution. Biotechnol Adv 2023; 68:108238. [PMID: 37619825 DOI: 10.1016/j.biotechadv.2023.108238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Directed enzyme evolution has revolutionized the rapid development of enzymes with desired properties. However, the lack of a high-throughput method to identify the most suitable variants from a large pool of genetic diversity poses a major bottleneck. To overcome this challenge, growth-coupled in vivo high-throughput selection approaches (GCHTS) have emerged as a novel selection system for enzyme evolution. GCHTS links the survival of the host cell with the properties of the target protein, resulting in a screening system that is easily measurable and has a high throughput-scale limited only by transformation efficiency. This allows for the rapid identification of desired variants from a pool of >109 variants in each experiment. In recent years, GCHTS approaches have been extensively utilized in the directed evolution of multiple enzymes, demonstrating success in catalyzing non-native substrates, enhancing catalytic activity, and acquiring novel functions. This review introduces three main strategies employed to achieve GCHTS: the elimination of toxic compounds via desired variants, enabling host cells to thrive in hazardous conditions; the complementation of an auxotroph with desired variants, where essential genes for cell growth have been eliminated; and the control of the transcription or expression of a reporter gene related to host cell growth, regulated by the desired variants. Additionally, we highlighted the recent developments in the in vivo continuous evolution of enzyme technology, including phage-assisted continuous evolution (PACE) and orthogonal DNA Replication (OrthoRep). Furthermore, this review discusses the challenges and future prospects in the field of growth-coupled selection for protein engineering.
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Affiliation(s)
- Zhengqun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuting Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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11
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Shrestha P, Rotatori S, Madden-Hennessey K, Mohammed C, Yang CH, Urbani J, Pettinelli J, Liu X, Zhao Q. Selective expansion of target cells using the Enrich TROVO platform. Biotechniques 2023; 75:56-64. [PMID: 37551835 PMCID: PMC10476488 DOI: 10.2144/btn-2023-0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
Enriching target cell clones from diverse cell populations is vital for many life science applications. We have developed a novel method to rapidly and efficiently purify specific clonal cell populations from a larger, heterogeneous group using the Enrich TroVo system (Enrich Biosystems Inc., CT, USA). This system takes advantage of microfabrication and optical technologies by utilizing small hydrogel wells to separate desired cell populations and an innovative patching technique to selectively eliminate undesired cells. This method allows the isolation and growth of desired cells with minimal impact on their viability and proliferation. We successfully isolated and expanded clonal cell populations of desired cells using two model cells. Compared with fluorescence-activated cell sorting, Enrich TroVo system offers a promising alternative for isolating of sensitive, adherent cells, that is, patient-derived cells.
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Affiliation(s)
- Prem Shrestha
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | - Stephen Rotatori
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | | | - Christina Mohammed
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | - Chi-han Yang
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | - Jordan Urbani
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | - Joseph Pettinelli
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | - Xueqi Liu
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
| | - Qi Zhao
- Enrich Biosystems Inc., 21 Business Park Drive, Suite 4, Branford, CT 06405, USA
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12
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Cheng G, Xiao Q, Kuan CY, Ho YP. On-demand light-driven release of droplets stabilized via a photoresponsive fluorosurfactant. MICROSYSTEMS & NANOENGINEERING 2023; 9:89. [PMID: 37448968 PMCID: PMC10336138 DOI: 10.1038/s41378-023-00567-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 06/03/2023] [Indexed: 07/18/2023]
Abstract
Water-in-oil droplets have emerged as promising microreactors for high-throughput biochemical analysis due to their features of reduced sample consumption and automated operation. For a typical screening application, droplets are often trapped for continuous monitoring of the reaction over an extended period, followed by the selective retrieval of targeted droplets based on the after-effect of biochemical reactions. While techniques for droplet trapping are well developed, retrieval of targeted droplets mainly demands complicated device fabrication or sophisticated control. Herein, facile and rapid selective droplet release is achieved by utilizing a new class of photoresponsive fluorosurfactant based on plasmonic nanoparticles. The intense photothermal response provided by this novel photoresponsive fluorosurfactant is capable of vaporizing the fluorocarbon oil at the droplet interface under laser illumination, resulting in a bubble releasing a trapped droplet on demand. A fully automated fluorescence-activated droplet release platform has also been developed to demonstrate its potential for droplet-based large-scale screening applications.
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Affiliation(s)
- Guangyao Cheng
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qinru Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chit Yau Kuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, 999077 China
- The Ministry of Education Key Laboratory of Regeneration Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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13
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Vitalis C, Wenzel T. Leveraging interactions in microfluidic droplets for enhanced biotechnology screens. Curr Opin Biotechnol 2023; 82:102966. [PMID: 37390513 DOI: 10.1016/j.copbio.2023.102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
Microfluidic droplet screens serve as an innovative platform for high-throughput biotechnology, enabling significant advancements in discovery, product optimization, and analysis. This review sheds light on the emerging trends of interaction assays in microfluidic droplets, underscoring the unique suitability of droplets for these applications. Encompassing a diverse range of biological entities such as antibodies, enzymes, DNA, RNA, various microbial and mammalian cell types, drugs, and other molecules, these assays demonstrate their versatility and scope. Recent methodological breakthroughs have escalated these screens to novel scales of bioanalysis and biotechnological product design. Moreover, we highlight pioneering advancements that extend droplet-based screens into new domains: cargo delivery within human bodies, application of synthetic gene circuits in natural environments, 3D printing, and the development of droplet structures responsive to environmental signals. The potential of this field is profound and only set to increase.
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Affiliation(s)
- Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile
| | - Tobias Wenzel
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile.
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14
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Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [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: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
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Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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15
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [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: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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16
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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17
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Liu J, Lyu X, Zhou Z, Yang L, Zeng J, Yang Y, Zhao Z, Chen R, Tong X, Li J, Liu H, Zou Y. Multifunctional Droplets Formed by Interfacially Self-Assembled Fluorinated Magnetic Nanoparticles for Biocompatible Single Cell Culture and Magnet-Driven Manipulation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:17324-17334. [PMID: 36962257 DOI: 10.1021/acsami.2c23003] [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: 06/18/2023]
Abstract
The ability to encapsulate and manipulate droplets with a picoliter volume of samples and reagents shows great potential for practical applications in chemistry, biology, and materials science. Magnetic control is a promising approach for droplet manipulation due to its ability for wireless control and its ease of implementation. However, it is challenged by the poor biocompatibility of magnetic materials in aqueous droplets. Moreover, current droplet technology is problematic because of the molecule leakage between droplets. In the paper, we propose multifunctional droplets with the surface coated by a layer of fluorinated magnetic nanoparticles for magnetically actuated droplet manipulation. Multifunctional droplets show excellent biocompatibility for cell culture, nonleakage of molecules, and high response to a magnetic field. We developed a strategy of coating the F-MNP@SiO2 on the outer surface of droplets instead of adding magnetic material into droplets to enable droplets with a highly magnetic response. The encapsulated bacteria and cells in droplets did not need to directly contact with the magnetic materials at the outer surface, showing high biocompatibility with living cells. These droplets can be precisely manipulated based on magnet distance, the time duration of the magnetic field, the droplet size, and the MNP composition, which well match with theoretical analysis. The precise magnetically actuated droplet manipulation shows great potential for accurate and sensitive droplet-based bioassays like single cell analysis.
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Affiliation(s)
- Jiahe Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoyan Lyu
- Department of Dermatology, Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ziwei Zhou
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Lin Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jie Zeng
- College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yao Yang
- Department of Dermatology, Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenghuan Zhao
- College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Rui Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xin Tong
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiaqi Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Hailan Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yuan Zou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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18
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France SP, Lewis RD, Martinez CA. The Evolving Nature of Biocatalysis in Pharmaceutical Research and Development. JACS AU 2023; 3:715-735. [PMID: 37006753 PMCID: PMC10052283 DOI: 10.1021/jacsau.2c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 06/19/2023]
Abstract
Biocatalysis is a highly valued enabling technology for pharmaceutical research and development as it can unlock synthetic routes to complex chiral motifs with unparalleled selectivity and efficiency. This perspective aims to review recent advances in the pharmaceutical implementation of biocatalysis across early and late-stage development with a focus on the implementation of processes for preparative-scale syntheses.
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19
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Cao Y, Tian J, Lin H, Li Q, Xiao Y, Cui H, Shum HC. Partitioning-Induced Isolation of Analyte and Analysis via Multiscaled Aqueous Two-Phase System. Anal Chem 2023; 95:4644-4652. [PMID: 36855862 DOI: 10.1021/acs.analchem.2c04861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Most fluorescence-based bioanalytical applications need labeling of analytes. Conventional labeling requires washing to remove the excess fluorescent labels and reduce the noise signals. These pretreatments are labor intensive and need specialized equipment, hindering portable applications in resource-limited areas. Herein, we use the aqueous two-phase system (ATPS) to realize the partitioning-induced isolation of labeled analytes from background signals without extra processing steps. ATPS is formed by mixing two polymers at sufficiently high concentrations. ATPS-based isolation is driven by intrinsic affinity differences between analytes and excess labels. To demonstrate the partitioning-induced isolation and analysis, fluorescein isothiocyanate (FITC) is selected as the interfering fluorophore, and a monoclonal antibody (IgG) is used as the analyte. To optimize ATPS compositions, different molecular weights and mass fractions of polyethylene glycol (PEG) and dextran and different phosphate-buffered saline (PBS) concentrations are investigated. Various operational scales of our approach are demonstrated, suggesting its compatibility with various bioanalytical applications. In centimeter-scale ATPS, the optimized distribution ratios of IgG and FITC are 91.682 and 0.998 using PEG 6000 Da and dextran 10,000 Da in 10 mM PBS. In millimeter-scale ATPS, the analyte is enriched to 6.067 fold using 15 wt % PEG 35,000 Da and 5 wt % dextran 500,000 Da in 10 mM PBS. In microscale ATPS, analyte dilutions are isolated into picoliter droplets, and the measured fluorescence intensities linearly correlated with the analyte concentrations (R2 = 0.982).
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Affiliation(s)
- Yang Cao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Jingxuan Tian
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Haisong Lin
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Qingchuan Li
- School of Chemistry and Chemical Engineering, National Engineering Research Center for Colloidal Materials, Shandong University, Jinan 250100, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Yang Xiao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Huanqing Cui
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
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20
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Zhang Z, Guo Q, Wang Y, Huang H. High-throughput screening of microbial strains in large-scale microfluidic droplets. Front Bioeng Biotechnol 2023; 11:1105277. [PMID: 36970622 PMCID: PMC10037112 DOI: 10.3389/fbioe.2023.1105277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
The transformation of engineered microbial cells is a pivotal link in green biomanufacturing. Its distinctive research application involves genetic modification of microbial chassis to impart targeted traits and functions for effective synthesis of the desired products. Microfluidics, as an emerging complementary solution, focuses on controlling and manipulating fluid in channels at the microscopic scale. One of its subcategories is droplet-based microfluidics (DMF), which can generate discrete droplets using immiscible multiphase fluids at kHz frequencies. To date, droplet microfluidics has been successfully applied to a variety of microbes, including bacteria, yeast, and filamentous fungi, and the detection of massive metabolites of strain products, such as polypeptides, enzymes, and lipids, has been realized. In summary, we firmly believe that droplet microfluidics has evolved into a powerful technology that will pave the way for high-throughput screening of engineered microbial strains in the green biomanufacturing industry.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang, China
| | - Qi Guo
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- *Correspondence: Yuetong Wang, ; He Huang,
| | - He Huang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- *Correspondence: Yuetong Wang, ; He Huang,
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21
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Review of the role of surfactant dynamics in drop microfluidics. Adv Colloid Interface Sci 2023; 312:102844. [PMID: 36708604 DOI: 10.1016/j.cis.2023.102844] [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: 11/15/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
Surfactants are employed in microfluidic systems not just for drop stabilisation, but also to study local phenomena in industrial processes. On the scale of a single drop, these include foaming, emulsification and stability of foams and emulsions using statistically significant ensembles of bubbles or drops respectively. In addition, surfactants are often a part of a formulation in microfluidic drop reactors. In all these applications, surfactant dynamics play a crucial role and need to be accounted for. In this review, the effect of surfactant dynamics is considered on the level of standard microfluidic operations: drop formation, movement in channels and coalescence, but also on a more general level, considering the mechanisms controlling surfactant adsorption on time- and length-scales characteristic of microfluidics. Some examples of relevant calculations are provided. The advantages and challenges of the use of microfluidics to measure dynamic interfacial tension at short time-scales are discussed.
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22
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Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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23
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Yanakieva D, Vollmer L, Kumar S, Becker S, Toleikis L, Pekar L, Kolmar H, Zielonka S, Krah S. One-Pot Droplet RT-OE-PCR for the Generation of Natively Paired Antibody Immune Libraries. Methods Mol Biol 2023; 2681:213-229. [PMID: 37405650 DOI: 10.1007/978-1-0716-3279-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Classical yeast surface display (YSD) antibody immune libraries are generated by a separate amplification of heavy- and light-chain antibody variable regions (VH and VL, respectively) and subsequent random recombination during the molecular cloning procedure. However, each B cell receptor comprises a unique VH-VL combination, which has been selected and affinity matured in vivo for optimal stability and antigen binding. Thus, the native variable chain pairing is important for the functioning and biophysical properties of the respective antibody. Herein, we present a method for the amplification of cognate VH-VL sequences, compatible with both next-generation sequencing (NGS) and YSD library cloning. We employ a single B cell encapsulation in water-in-oil droplets, followed by a one-pot reverse transcription overlap extension PCR (RT-OE-PCR), resulting in a paired VH-VL repertoire from more than a million B cells in a single day.
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Affiliation(s)
- Desislava Yanakieva
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lena Vollmer
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Satyendra Kumar
- Protein Engineering and Antibody Technologies (PEAT), EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Stefan Becker
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany.
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24
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Cowell T, Han HS. Double Emulsion Flow Cytometry for Rapid Single Genome Detection. Methods Mol Biol 2023; 2689:155-167. [PMID: 37430053 DOI: 10.1007/978-1-0716-3323-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Established techniques in droplet microfluidics have utilized single emulsion (SE) drops to compartmentalize and analyze single cells achieving high-throughput, low input analysis. Building upon this foundation, double emulsion (DE) droplet microfluidics has emerged with distinct advantages in terms of stable compartmentalization, resistance to merging, and most importantly direct compatibility with flow cytometry. In this chapter, we describe a simple-to-fabricate, single-layer DE drop generation device that achieves spatial control over surface wetting with a plasma treatment step. This easy-to-operate device allows for the robust production of single-core DEs with excellent control over the monodispersity. We further explain the use of these DE drops for single-molecule and single-cell assays. Detailed protocols are described to perform single molecule detection using droplet digital PCR in DE drops and automated detection of DE drops on a fluorescence-activated cell sorter (FACS). Due to the wide availability of FACS instruments, DE methods can facilitate the broader adoption of drop-based screening. As the applications of FACS-compatible DE droplets are immensely varied and extend well beyond what can be explored here, this chapter should be seen as an introduction to DE microfluidics.
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Affiliation(s)
- Thomas Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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25
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A growth selection system for the directed evolution of amine-forming or converting enzymes. Nat Commun 2022; 13:7458. [PMID: 36460668 PMCID: PMC9718777 DOI: 10.1038/s41467-022-35228-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Fast screening of enzyme variants is crucial for tailoring biocatalysts for the asymmetric synthesis of non-natural chiral chemicals, such as amines. However, most existing screening methods either are limited by the throughput or require specialized equipment. Herein, we report a simple, high-throughput, low-equipment dependent, and generally applicable growth selection system for engineering amine-forming or converting enzymes and apply it to improve biocatalysts belonging to three different enzyme classes. This results in (i) an amine transaminase variant with 110-fold increased specific activity for the asymmetric synthesis of the chiral amine intermediate of Linagliptin; (ii) a 270-fold improved monoamine oxidase to prepare the chiral amine intermediate of Cinacalcet by deracemization; and (iii) an ammonia lyase variant with a 26-fold increased activity in the asymmetric synthesis of a non-natural amino acid. Our growth selection system is adaptable to different enzyme classes, varying levels of enzyme activities, and thus a flexible tool for various stages of an engineering campaign.
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26
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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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27
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Yi J, Li Z. Artificial multi-enzyme cascades for natural product synthesis. Curr Opin Biotechnol 2022; 78:102831. [PMID: 36308987 DOI: 10.1016/j.copbio.2022.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022]
Abstract
Artificial multi-enzyme cascades bear great potential for offering sustainable synthesis of useful and valuable natural molecules. In the past two years, many new cascades were developed to produce natural alcohols, acids, esters, amino compounds, fatty acid derivatives, alkaloids, terpenoids, terpenes and monosaccharides from natural substrates and simple chemicals, respectively. These artificial cascades were constructed by combining individual enzymes designed using the retro-synthesis strategy and based on the available natural substrates and simple chemicals. While performing the cascades in vivo is often simple and straightforward, in vitro cascades usually require cofactor regeneration that was achieved by introducing one or more cofactor-regeneration modules in one pot. Protein engineering is frequently used to improve the performances of some enzymes in the cascades.
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Affiliation(s)
- Jieran Yi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
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28
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Vallapurackal J, Stucki A, Liang AD, Klehr J, Dittrich PS, Ward TR. Ultrahigh-Throughput Screening of an Artificial Metalloenzyme using Double Emulsions. Angew Chem Int Ed Engl 2022; 61:e202207328. [PMID: 36130864 PMCID: PMC9828110 DOI: 10.1002/anie.202207328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 01/12/2023]
Abstract
The potential for ultrahigh-throughput compartmentalization renders droplet microfluidics an attractive tool for the directed evolution of enzymes. Importantly, it ensures maintenance of the phenotype-genotype linkage, enabling reliable identification of improved mutants. Herein, we report an approach for ultrahigh-throughput screening of an artificial metalloenzyme in double emulsion droplets (DEs) using commercially available fluorescence-activated cell sorters (FACS). This protocol was validated by screening a 400 double-mutant streptavidin library for ruthenium-catalyzed deallylation of an alloc-protected aminocoumarin. The most active variants, identified by next-generation sequencing, were in good agreement with hits obtained using a 96-well plate procedure. These findings pave the way for the systematic implementation of FACS for the directed evolution of (artificial) enzymes and will significantly expand the accessibility of ultrahigh-throughput DE screening protocols.
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Affiliation(s)
- Jaicy Vallapurackal
- Department of ChemistryUniversity of BaselMattenstrasse 24a4058BaselSwitzerland,National Competence Center in Research (NCCR) Molecular Systems EngineeringBaselSwitzerland
| | - Ariane Stucki
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 264058BaselSwitzerland,National Competence Center in Research (NCCR) Molecular Systems EngineeringBaselSwitzerland
| | - Alexandria Deliz Liang
- Department of ChemistryUniversity of BaselMattenstrasse 24a4058BaselSwitzerland,National Competence Center in Research (NCCR) Molecular Systems EngineeringBaselSwitzerland
| | - Juliane Klehr
- Department of ChemistryUniversity of BaselMattenstrasse 24a4058BaselSwitzerland,National Competence Center in Research (NCCR) Molecular Systems EngineeringBaselSwitzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 264058BaselSwitzerland,National Competence Center in Research (NCCR) Molecular Systems EngineeringBaselSwitzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of BaselMattenstrasse 24a4058BaselSwitzerland,National Competence Center in Research (NCCR) Molecular Systems EngineeringBaselSwitzerland
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29
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Su X, Yang J, Yuan H, Liu C, Tu R, Liu P, Wang Q, Zhu L. Directed Evolution of Laccase for Improved Thermal Stability Facilitated by Droplet-Based Microfluidic Screening System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13700-13708. [PMID: 36239441 DOI: 10.1021/acs.jafc.2c05048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Laccases are attractive biocatalysts for industry due to their broad substrate spectrum, the use of oxygen as final electron acceptor, and water as the sole byproduct. Increasing efforts have been devoted to the engineering of laccases to improve their properties. The droplet-based microfluidic screening (DMFS) technology can accelerate the screening procedure and probe the large sequence space. In this study, a DMFS system including a heating step and picoinjection was used to sort large laccase libraries, yielding 12 variants with enhanced thermotolerance. All the obtained amino acid substitutions are distributed on the surface of the laccase. Interestingly, recombination of three identified substitutions of Asp to Asn on the surface resulted in the best variant M20, exhibiting 24.0-fold higher remaining activity at 58.8 °C and 1.9-3.4-fold higher remaining activity after incubation in organic solvents solution (20% (v/v) methanol and ethanol) and ionic liquid solution (20% (v/v) 1-ethyl-3-methylimidazolium ethyl sulfate) for 12 h. Furthermore, molecular dynamic simulations revealed that the recombination of the three beneficial substitutions, Asp98Asn, Asp474Asn, and Asp340Asn on the surface introduced more hydrogen bonds compared to the wild type, which made M20 more thermostable. This study highlighted the importance of the DMFS system for an efficient identification of beneficial long-distance amino acid substitutions.
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Affiliation(s)
- Xiaolan Su
- University of Science and Technology of China, 96 JinZhai Road, Baohe District, Hefei 230026, Anhui, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Jianhua Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Huiling Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Cui Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
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30
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Morellon-Sterling R, Bolivar JM, Fernandez-Lafuente R. Switch off/switch on of a cysteinyl protease as a way to preserve the active catalytic group by modification with a reversible covalent thiol modifier: Immobilization of ficin on vinyl-sulfone activated supports. Int J Biol Macromol 2022; 220:1155-1162. [PMID: 36037909 DOI: 10.1016/j.ijbiomac.2022.08.155] [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: 05/23/2022] [Revised: 08/11/2022] [Accepted: 08/23/2022] [Indexed: 11/05/2022]
Abstract
The immobilization of ficin (a cysteinyl proteases) on vinyl sulfone agarose produced its almost full inactivation. It was observed that the incubation of the free and immobilized enzyme in β-mercaptoethanol produced a 20 % of enzyme activity recovery, suggesting that the inactivation due to the immobilization could be a consequence of the modification of the catalytic Cys. To prevent the enzyme inactivation during the immobilization, switching off of ficin via Cys reaction with dipyridyl-disulfide was implemented, giving a reversible disulfide bond that produced a fully inactive enzyme. The switch on of ficin activity was implemented by incubation in 1 M β-mercaptoethanol. Using this strategy to immobilize the enzyme on vinyl sulfone agarose beads, the expressed activity of the immobilized ficin could be boosted up to 80 %. The immobilized enzyme presented a thermal stabilization similar to that obtained using ficin-glyoxyl-agarose beads. This procedure may be extended to many enzymes containing critical Cys, to permit their immobilization or chemical modification.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Juan M Bolivar
- FQPIMA Group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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31
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Zhuang Y, Cheng S, Kovalchuk N, Simmons M, Matar OK, Guo YK, Arcucci R. Ensemble latent assimilation with deep learning surrogate model: application to drop interaction in a microfluidics device. LAB ON A CHIP 2022; 22:3187-3202. [PMID: 35875987 DOI: 10.1039/d2lc00303a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A major challenge in the field of microfluidics is to predict and control drop interactions. This work develops an image-based data-driven model to forecast drop dynamics based on experiments performed on a microfluidics device. Reduced-order modelling techniques are applied to compress the recorded images into low-dimensional spaces and alleviate the computational cost. Recurrent neural networks are then employed to build a surrogate model of drop interactions by learning the dynamics of compressed variables in the reduced-order space. The surrogate model is integrated with real-time observations using data assimilation. In this paper we developed an ensemble-based latent assimilation algorithm scheme which shows an improvement in terms of accuracy with respect to the previous approaches. This work demonstrates the possibility to create a reliable data-driven model enabling a high fidelity prediction of drop interactions in microfluidics device. The performance of the developed system is evaluated against experimental data (i.e., recorded videos), which are excluded from the training of the surrogate model. The developed scheme is general and can be applied to other dynamical systems.
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Affiliation(s)
- Yilin Zhuang
- Department of Chemical Engineering Imperial College London, UK
| | - Sibo Cheng
- Data Science Institute, Department of Computing, Imperial College London, UK.
| | - Nina Kovalchuk
- School of Chemical Engineering, University of Birmingham, UK
| | - Mark Simmons
- School of Chemical Engineering, University of Birmingham, UK
| | - Omar K Matar
- Department of Chemical Engineering Imperial College London, UK
| | - Yi-Ke Guo
- Data Science Institute, Department of Computing, Imperial College London, UK.
| | - Rossella Arcucci
- Data Science Institute, Department of Computing, Imperial College London, UK.
- Department of Earth Science & Engineering, Imperial College London, UK
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32
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Cowell TW, Dobria A, Han HS. Simplified, Shear Induced Generation of Double Emulsions for Robust Compartmentalization during Single Genome Analysis. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20528-20537. [PMID: 35502700 DOI: 10.1021/acsami.1c22692] [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: 06/14/2023]
Abstract
Drop microfluidics has driven innovations for high throughput, low input analysis techniques such as single-cell RNA-seq. However, the instability of single emulsion (SE) drops occasionally causes significant merging during drop processing, limiting most applications to single-step reactions in drops. Here, we show that double emulsion (DE) drops address this critical limitation and completely prevent drop contents from mixing. DEs show excellent stability during thermal cycling. More importantly, DEs undergo rupture into the continuous phase instead of merging, preventing content mixing and eliminating unstable drops from the downstream analysis. Due to the lack of drop merging, the monodispersity of drops is maintained throughout a workflow, enabling the deterministic manipulation of drops downstream. We also developed a simple, one-layer DE drop maker compatible with simple surface treatment using a plasma cleaner. The device allows for the robust production of single-core DEs at a wide range of flow rates and better control over the shell thickness, both of which have been significant limitations of conventional two-layer devices. This approach makes the fabrication of DE devices much more accessible, facilitating its broader adoption. Finally, we show that DE droplets eliminate content mixing and maintain compartmentalization of single virus genomes during PCR-based amplification and barcoding, while SEs mixed contents due to merging. With their resistance to content mixing, DE drops have key advantages for multistep reactions in drops, which is limited in SEs due to merging and content mixing.
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Affiliation(s)
- Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Andrew Dobria
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Ave., Urbana, Illinois 61801, United States
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33
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Sierra AMR, Arold ST, Grünberg R. Efficient multi-gene expression in cell-free droplet microreactors. PLoS One 2022; 17:e0260420. [PMID: 35312702 PMCID: PMC8936439 DOI: 10.1371/journal.pone.0260420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-free transcription and translation systems promise to accelerate and simplify the engineering of proteins, biological circuits and metabolic pathways. Their encapsulation on microfluidic platforms can generate millions of cell-free reactions in picoliter volume droplets. However, current methods struggle to create DNA diversity between droplets while also reaching sufficient protein expression levels. In particular, efficient multi-gene expression has remained elusive. We here demonstrate that co-encapsulation of DNA-coated beads with a defined cell-free system allows high protein expression while also supporting genetic diversity between individual droplets. We optimize DNA loading on commercially available microbeads through direct binding as well as through the sequential coupling of up to three genes via a solid-phase Golden Gate assembly or BxB1 integrase-based recombineering. Encapsulation with an off-the-shelf microfluidics device allows for single or multiple protein expression from a single DNA-coated bead per 14 pL droplet. We envision that this approach will help to scale up and parallelize the rapid prototyping of more complex biological systems.
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Affiliation(s)
- Ana Maria Restrepo Sierra
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Bionanoscience Department/Applied Sciences, Technische Universiteit Delft, Delft, The Netherlands
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Centre de Biologie Structurale (CBS)/CNRS/INSERM, Université Montpellier, Montpellier, France
| | - Raik Grünberg
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- * E-mail:
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34
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Duncombe TA, Ponti A, Seebeck FP, Dittrich PS. UV-Vis Spectra-Activated Droplet Sorting for Label-Free Chemical Identification and Collection of Droplets. Anal Chem 2021; 93:13008-13013. [PMID: 34533299 DOI: 10.1021/acs.analchem.1c02822] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We introduce the UV-vis spectra-activated droplet sorter (UVADS) for high-throughput label-free chemical identification and enzyme screening. In contrast to previous absorbance-based droplet sorters that relied on single-wavelength absorbance in the visible range, our platform collects full UV-vis spectra from 200 to 1050 nm at up to 2100 spectra per second. Our custom-built open-source software application, "SpectraSorter," enables real-time data processing, analysis, visualization, and selection of droplets for sorting with any set of UV-vis spectral features. An optimized UV-vis detection region extended the absorbance path length for droplets and allowed for the direct protein quantification down to 10 μM of bovine serum albumin at 280 nm. UV-vis spectral data can distinguish a variety of different chemicals or spurious events (such as air bubbles) that are inaccessible at a single wavelength. The platform is used to measure ergothionase enzyme activity from monoclonal microcolonies isolated in droplets. In a label-free manner, we directly measure the ergothioneine substrate to thiourocanic acid product conversion while tracking the microcolony formation. UVADS represents an important new tool for high-throughput label-free in-droplet chemical analysis.
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Affiliation(s)
- Todd A Duncombe
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.,NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Aaron Ponti
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Florian P Seebeck
- NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.,Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002 Basel, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.,NCCR Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
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