1
|
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.
Collapse
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
| |
Collapse
|
2
|
Droplet-based optofluidic systems for measuring enzyme kinetics. Anal Bioanal Chem 2019; 412:3265-3283. [PMID: 31853606 DOI: 10.1007/s00216-019-02294-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 01/05/2023]
Abstract
The study of enzyme kinetics is of high significance in understanding metabolic networks in living cells and using enzymes in industrial applications. To gain insight into the catalytic mechanisms of enzymes, it is necessary to screen an enormous number of reaction conditions, a process that is typically laborious, time-consuming, and costly when using conventional measurement techniques. In recent times, droplet-based microfluidic systems have proved themselves to be of great utility in large-scale biological experimentation, since they consume a minimal sample, operate at high analytical throughput, are characterized by efficient mass and heat transfer, and offer high levels of integration and automation. The primary goal of this review is the introduction of novel microfluidic tools and detection methods for use in high-throughput and sensitive analysis of enzyme kinetics. The first part of this review focuses on introducing basic concepts of enzyme kinetics and describing most common microfluidic approaches, with a particular focus on segmented flow. Herein, the key advantages include accurate control over the flow behavior, efficient mass and heat transfer, multiplexing, and high-level integration with detection modalities. The second part describes the current state-of-the-art platforms for high-throughput and sensitive analysis of enzyme kinetics. In addition to our categorization of recent advances in measuring enzyme kinetics, we have endeavored to critically assess the limitations of each of these detection approaches and propose strategies to improve measurements in droplet-based microfluidics. Graphical abstract.
Collapse
|
3
|
Buryska T, Vasina M, Gielen F, Vanacek P, van Vliet L, Jezek J, Pilat Z, Zemanek P, Damborsky J, Hollfelder F, Prokop Z. Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics. Anal Chem 2019; 91:10008-10015. [PMID: 31240908 DOI: 10.1021/acs.analchem.9b01839] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Functional annotation of novel proteins lags behind the number of sequences discovered by the next-generation sequencing. The throughput of conventional testing methods is far too low compared to sequencing; thus, experimental alternatives are needed. Microfluidics offer high throughput and reduced sample consumption as a tool to keep up with a sequence-based exploration of protein diversity. The most promising droplet-based systems have a significant limitation: leakage of hydrophobic compounds from water compartments to the carrier prevents their use with hydrophilic reagents. Here, we present a novel approach of substrate delivery into microfluidic droplets and apply it to high-throughput functional characterization of enzymes that convert hydrophobic substrates. Substrate delivery is based on the partitioning of hydrophobic chemicals between the oil and water phases. We applied a controlled distribution of 27 hydrophobic haloalkanes from oil to reaction water droplets to perform substrate specificity screening of eight model enzymes from the haloalkane dehalogenase family. This droplet-on-demand microfluidic system reduces the reaction volume 65 000-times and increases the analysis speed almost 100-fold compared to the classical test tube assay. Additionally, the microfluidic setup enables a convenient analysis of dependences of activity on the temperature in a range of 5 to 90 °C for a set of mesophilic and hyperstable enzyme variants. A high correlation between the microfluidic and test tube data supports the approach robustness. The precision is coupled to a considerable throughput of >20 000 reactions per day and will be especially useful for extending the scope of microfluidic applications for high-throughput analysis of reactions including compounds with limited water solubility.
Collapse
Affiliation(s)
- Tomas Buryska
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Fabrice Gielen
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom.,Living Systems Institute , University of Exeter , Exeter EX4 4QD , United Kingdom
| | - Pavel Vanacek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Liisa van Vliet
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Jan Jezek
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Zdenek Pilat
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Pavel Zemanek
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Florian Hollfelder
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| |
Collapse
|
4
|
Shojaeian M, Lehr FX, Göringer HU, Hardt S. On-Demand Production of Femtoliter Drops in Microchannels and Their Use as Biological Reaction Compartments. Anal Chem 2019; 91:3484-3491. [DOI: 10.1021/acs.analchem.8b05063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
5
|
Hassan SU, Nightingale AM, Niu X. Micromachined optical flow cell for sensitive measurement of droplets in tubing. Biomed Microdevices 2018; 20:92. [PMID: 30370472 PMCID: PMC6208900 DOI: 10.1007/s10544-018-0337-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here a micromachined flow cell with enhanced optical sensitivity is presented that allows high-throughput analysis of microdroplets. As a droplet flows through multiple concatenated measurement points, the rate of enzymatic reaction in the droplet can be fully characterized without stopping the flow. Since there is no cross-talk between the droplets, the flow cell is capable of continuously measuring biochemical assays in a droplet flow and thus is suitable to be used for continuous point-of-care diagnostics monitoring. This paper describes the design and operation of the device and its validation by application to the accurate and continuous quantification of glucose concentrations using an oxidase enzymatic assay. The flow cell forms an important component in the miniaturization of chemical and bio analyzers into portable or wearable devices.
Collapse
Affiliation(s)
- Sammer-Ul Hassan
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK. .,Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Adrian M Nightingale
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK.,Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Xize Niu
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK.,Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| |
Collapse
|
6
|
Hassan SU, Nightingale AM, Niu X. Continuous measurement of enzymatic kinetics in droplet flow for point-of-care monitoring. Analyst 2018; 141:3266-73. [PMID: 27007645 DOI: 10.1039/c6an00620e] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Droplet microfluidics is ideally suited to continuous biochemical analysis, requiring low sample volumes and offering high temporal resolution. Many biochemical assays are based on enzymatic reactions, the kinetics of which can be obtained by probing droplets at multiple points over time. Here we present a miniaturised multi-detector flow cell to analyse enzyme kinetics in droplets, with an example application of continuous glucose measurement. Reaction rates and Michaelis-Menten kinetics can be quantified for each individual droplet and unknown glucose concentrations can be accurately determined (errors <5%). Droplets can be probed continuously giving short sample-to-result time (∼30 s) measurement. In contrast to previous reports of multipoint droplet measurement (all of which used bulky microscope-based setups) the flow cell presented here has a small footprint and uses low-powered, low-cost components, making it ideally suited for use in field-deployable devices.
Collapse
Affiliation(s)
- Sammer-Ul Hassan
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Adrian M Nightingale
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Xize Niu
- Faculty of Engineering and the Environment, University of Southampton, Southampton, SO17 1BJ, UK. and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| |
Collapse
|
7
|
Abstract
Combinatorial drug treatment strategies perturb biological networks synergistically to achieve therapeutic effects and represent major opportunities to develop advanced treatments across a variety of human disease areas. However, the discovery of new combinatorial treatments is challenged by the sheer scale of combinatorial chemical space. Here, we report a high-throughput system for nanoliter-scale phenotypic screening that formulates a chemical library in nanoliter droplet emulsions and automates the construction of chemical combinations en masse using parallel droplet processing. We applied this system to predict synergy between more than 4,000 investigational and approved drugs and a panel of 10 antibiotics against Escherichia coli, a model gram-negative pathogen. We found a range of drugs not previously indicated for infectious disease that synergize with antibiotics. Our validated hits include drugs that synergize with the antibiotics vancomycin, erythromycin, and novobiocin, which are used against gram-positive bacteria but are not effective by themselves to resolve gram-negative infections.
Collapse
|
8
|
|
9
|
Dressler OJ, Casadevall I Solvas X, deMello AJ. Chemical and Biological Dynamics Using Droplet-Based Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:1-24. [PMID: 28375703 DOI: 10.1146/annurev-anchem-061516-045219] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas. We then discuss a wide range of analytical methods that have been successfully adapted for analyte detection in droplets. Finally, we highlight a diversity of studies where droplet-based microfluidic strategies have enabled the characterization of dynamic systems that would otherwise have remained unexplorable.
Collapse
Affiliation(s)
- Oliver J Dressler
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland;
| | | | - Andrew J deMello
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland;
| |
Collapse
|
10
|
Kaminski TS, Garstecki P. Controlled droplet microfluidic systems for multistep chemical and biological assays. Chem Soc Rev 2017; 46:6210-6226. [DOI: 10.1039/c5cs00717h] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Droplet microfluidics is a relatively new and rapidly evolving field of science focused on studying the hydrodynamics and properties of biphasic flows at the microscale, and on the development of systems for practical applications in chemistry, biology and materials science.
Collapse
Affiliation(s)
- T. S. Kaminski
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| | - P. Garstecki
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
| |
Collapse
|
11
|
Bakalis E, Soldà A, Kosmas M, Rapino S, Zerbetto F. Complex Media and Enzymatic Kinetics. Anal Chem 2016; 88:5790-6. [DOI: 10.1021/acs.analchem.6b00343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Evangelos Bakalis
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126, Bologna, Italy
| | - Alice Soldà
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126, Bologna, Italy
| | - Marios Kosmas
- Department
of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Stefania Rapino
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126, Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, V. F. Selmi 2, 40126, Bologna, Italy
| |
Collapse
|