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Vladisaljević GT. Droplet Microfluidics for High-Throughput Screening and Directed Evolution of Biomolecules. MICROMACHINES 2024; 15:971. [PMID: 39203623 PMCID: PMC11356158 DOI: 10.3390/mi15080971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024]
Abstract
Directed evolution is a powerful technique for creating biomolecules such as proteins and nucleic acids with tailor-made properties for therapeutic and industrial applications by mimicking the natural evolution processes in the laboratory. Droplet microfluidics improved classical directed evolution by enabling time-consuming and laborious steps in this iterative process to be performed within monodispersed droplets in a highly controlled and automated manner. Droplet microfluidic chips can generate, manipulate, and sort individual droplets at kilohertz rates in a user-defined microchannel geometry, allowing new strategies for high-throughput screening and evolution of biomolecules. In this review, we discuss directed evolution studies in which droplet-based microfluidic systems were used to screen and improve the functional properties of biomolecules. We provide a systematic overview of basic on-chip fluidic operations, including reagent mixing by merging continuous fluid streams and droplet pairs, reagent addition by picoinjection, droplet generation, droplet incubation in delay lines, chambers and hydrodynamic traps, and droplet sorting techniques. Various microfluidic strategies for directed evolution using single and multiple emulsions and biomimetic materials (giant lipid vesicles, microgels, and microcapsules) are highlighted. Completely cell-free microfluidic-assisted in vitro compartmentalization methods that eliminate the need to clone DNA into cells after each round of mutagenesis are also presented.
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Affiliation(s)
- Goran T Vladisaljević
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, UK
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2
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Xin Y, Foster SW, Makey DM, Parker D, Bradow J, Wang X, Berritt S, Mongillo R, Grinias JP, Kennedy RT. High-Throughput Capillary Liquid Chromatography Using a Droplet Injection and Application to Reaction Screening. Anal Chem 2024; 96:4693-4701. [PMID: 38442211 PMCID: PMC11001260 DOI: 10.1021/acs.analchem.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The cycle time of a standard liquid chromatography (LC) system is the sum of the time for the chromatographic run and the autosampler injection sequence. Although LC separation times in the 1-10 s range have been demonstrated, injection sequences are commonly >15 s, limiting throughput possible with LC separations. Further, such separations are performed on relatively large bore columns requiring flow rates of ≥5 mL/min, thus generating large volumes of mobile phase waste when used for large scale screening and increasing the difficulty in interfacing to mass spectrometry. Here, a droplet injector system was established that replaces the autosampler with a four-port, two-position valve equipped with a 20 nL internal loop interfaced to a syringe pump and a three-axis positioner to withdraw sample droplets from a well plate. In the system, sample and immiscible fluid are pulled alternately from a well plate into a capillary and then through the injection valve. The valve is actuated when sample fills the loop to allow sequential injection of samples at high throughput. Capillary LC columns with 300 μm inner diameter were used to reduce the consumption of mobile phase and sample. The system achieved 96 separations of 20 nL droplet samples containing 3 components in as little as 8.1 min with 5-s cycle time. This system was coupled to a mass spectrometer through an electrospray ionization source for high-throughput chemical reaction screening.
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Affiliation(s)
- Yue Xin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel W Foster
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Deklin Parker
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - James Bradow
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Xiaochun Wang
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Simon Berritt
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Robert Mongillo
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, 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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Minami M, Nakata S, Uchimura T. Sample preparation conditions for the real-time measurement of W/O emulsions by resonance-enhanced multiphoton ionization time-of-flight mass spectrometry. ANAL SCI 2024; 40:573-577. [PMID: 38194211 PMCID: PMC10894760 DOI: 10.1007/s44211-023-00486-3] [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: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Analysis of an emulsion in its original dispersed condition is quite important for quality assessment and quality control. In the present study, the practical experimental conditions of the real-time measurement of a water-in-oil (W/O) emulsion were examined via resonance-enhanced multiphoton ionization time-of-flight mass spectrometry (REMPI-TOFMS). A W/O emulsion was prepared using cyclohexane as the oil phase with toluene as an analyte species. A time profile of the peak area for toluene was constructed based on the mass spectra. Normally, the negative spikes of a base signal are detected in a time profile when analyte molecules are dispersed in an oil phase. In this case, however, the positive spikes were unexpectedly detected rather than the negative ones. Though several factors could be relevant for the occurrence of the positive spikes, these spikes could have been suppressed by the addition of a small amount of n-alkane when the oil phase was prepared in the present study. The practical experimental conditions for the analysis of a W/O emulsion in real-time revealed that this method would be applicable to the analysis of an oil-in-water-in-oil (O/W/O) emulsion where the outer phase is also an oil phase.
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Affiliation(s)
- Minori Minami
- Department of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Shion Nakata
- Department of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Tomohiro Uchimura
- Department of Materials Science and Engineering, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.
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Payne EM, Murray BE, Penabad LI, Abbate E, Kennedy RT. Mass-Activated Droplet Sorting for the Selection of Lysine-Producing Escherichia coli. Anal Chem 2023; 95:15716-15724. [PMID: 37820298 PMCID: PMC11025463 DOI: 10.1021/acs.analchem.3c03080] [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: 10/13/2023]
Abstract
Synthetic biology relies on engineering cells to have desirable properties, such as the production of select chemicals. A bottleneck in engineering methods is often the need to screen and sort variant libraries for potential activity. Droplet microfluidics is a method for high-throughput sample preparation and analysis which has the potential to improve the engineering of cells, but a limitation has been the reliance on fluorescent analysis. Here, we show the ability to select cell variants grown in 20 nL droplets at 0.5 samples/s using mass-activated droplet sorting (MADS), a method for selecting droplets based on the signal intensity measured by electrospray ionization mass spectrometry (ESI-MS). Escherichia coli variants producing lysine were used to evaluate the applicability of MADS for synthetic biology. E. coli were shown to be effectively grown in droplets, and the lysine produced by these cells was detectable using ESI-MS. Sorting of lysine-producing cells based on the MS signal was shown, yielding 96-98% purity for high-producing variants in the selected pool. Using this technique, cells were recovered after screening, enabling downstream validation via phenotyping. The presented method is translatable to whole-cell engineering for biocatalyst production.
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Affiliation(s)
- Emory M. Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Bridget E. Murray
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Laura I. Penabad
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Eric Abbate
- Applications Development, Inscripta Inc., Pleasanton, CA 94588
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
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Schirmer M, Dusny C. Microbial single-cell mass spectrometry: status, challenges, and prospects. Curr Opin Biotechnol 2023; 83:102977. [PMID: 37515936 DOI: 10.1016/j.copbio.2023.102977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023]
Abstract
Single-cell analysis uncovers phenotypic differences between cells in a population and dissects their individual physiological states and differences on all omics levels from genome to phenome. Spectrometric observation allows label-free analysis of the metabolome and proteome of individual cells, but is still mainly limited to the analysis of mammalian single cells. Recent progress in mass spectrometry approaches now enables the analysis of microbial single cells - mainly by miniaturizing cell handling, incubation, and improving chip-coupling concepts for analyte ionization by interfacing microfluidic chips and mass spectrometers. This review aims at distilling the enabling principles behind microbial single-cell mass spectrometry and puts them into perspective for the future of the field.
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Affiliation(s)
- Martin Schirmer
- Department of Solar Materials - Microscale Analysis and Engineering, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Leizpig, Germany
| | - Christian Dusny
- Department of Solar Materials - Microscale Analysis and Engineering, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Leizpig, Germany.
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Fitzgerald P, Cochrane WG, Paegel BM. Dose-Response Activity-Based DNA-Encoded Library Screening. ACS Med Chem Lett 2023; 14:1295-1303. [PMID: 37736190 PMCID: PMC10510511 DOI: 10.1021/acsmedchemlett.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Dose-response, or "conforming" behavior, increases confidence in a screening hit's authenticity. Here, we demonstrate dose-response solid-phase DNA-encoded library (DEL) screening. Compound dose in microfluidic droplets is modulated via the UV intensity of photocleavage from DEL beads. A 55,296-member DEL was screened at different UV intensities against model enzyme drug targets factor Xa (FXa) and autotaxin (ATX). Both screens yielded photochemical dose-dependent hit rates (FXa hit rates of 0.08/0.05% at 100/30% UV exposure; ATX hit rates of 0.24/0.08% at 100/20% UV exposure). FXa hits contained structures reflective of FXa inhibitors and four hits inhibited FXa (IC50 = 4.2 ± 0.1, 7.4 ± 0.3, 9.0 ± 0.3, and 19 ± 2 μM.) The top ATX hits (two dihydrobenzamidazolones and a tetrahydroisoquinoline) were validated as inhibitors (IC50 = 7 ± 2, 13 ± 2, and 1 ± 0.3 μM). Photochemical dose-response DEL screening data prioritized hits for synthesis, the rate-limiting step in DEL lead identification.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Wesley G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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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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