51
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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.
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52
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Droplet-Based Microfluidics Methods for Detecting Enzyme Inhibitors. Methods Mol Biol 2019. [PMID: 31773657 DOI: 10.1007/978-1-0716-0163-1_14] [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: 10/17/2023]
Abstract
Sub-nanoliter droplets produced in microfluidic devices have gained an enormous importance for performing all kinds of biochemical assays. One of the main reasons is that the amounts of reagents employed can be reduced in approximately five orders of magnitude compared to conventional microplate assays. In this chapter, we describe how to carry out the design, fabrication, and operation of a microfluidic device that allows performing enzyme kinetics and enzyme inhibition assays in droplets. This procedure can be used effectively to screen a small size library of compounds. Then, we describe how to use this droplet microfluidic setup to screen for potential inhibitor compounds eluted from a coupled high-performance liquid chromatography (HPLC) system that separates crude natural extracts.
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53
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Philip D. Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
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54
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Xiao M, Zou K, Li L, Wang L, Tian Y, Fan C, Pei H. Stochastic DNA Walkers in Droplets for Super‐Multiplexed Bacterial Phenotype Detection. Angew Chem Int Ed Engl 2019; 58:15448-15454. [DOI: 10.1002/anie.201906438] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/12/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Kui Zou
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Lihua Wang
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Chunhai Fan
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 200240 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
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55
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Xiao M, Zou K, Li L, Wang L, Tian Y, Fan C, Pei H. Stochastic DNA Walkers in Droplets for Super‐Multiplexed Bacterial Phenotype Detection. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906438] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Kui Zou
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Lihua Wang
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
| | - Chunhai Fan
- Department School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University 500 Dongchuan Road Shanghai 200241 P. R. China
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56
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Chiu FWY, Stavrakis S. High-throughput droplet-based microfluidics for directed evolution of enzymes. Electrophoresis 2019; 40:2860-2872. [PMID: 31433062 PMCID: PMC6899980 DOI: 10.1002/elps.201900222] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023]
Abstract
Natural enzymes have evolved over millions of years to allow for their effective operation within specific environments. However, it is significant to note that despite their wide structural and chemical diversity, relatively few natural enzymes have been successfully applied to industrial processes. To address this limitation, directed evolution (DE) (a method that mimics the process of natural selection to evolve proteins toward a user‐defined goal) coupled with droplet‐based microfluidics allows the detailed analysis of millions of enzyme variants on ultra‐short timescales, and thus the design of novel enzymes with bespoke properties. In this review, we aim at presenting the development of DE over the last years and highlighting the most important advancements in droplet‐based microfluidics, made in this context towards the high‐throughput demands of enzyme optimization. Specifically, an overview of the range of microfluidic unit operations available for the construction of DE platforms is provided, focusing on their suitability and benefits for cell‐based assays, as in the case of directed evolution experimentations.
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Affiliation(s)
- Flora W Y Chiu
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
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57
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Sun M, Li Z, Wang S, Maryu G, Yang Q. Building Dynamic Cellular Machineries in Droplet-Based Artificial Cells with Single-Droplet Tracking and Analysis. Anal Chem 2019; 91:9813-9818. [PMID: 31284720 PMCID: PMC7260773 DOI: 10.1021/acs.analchem.9b01481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the application of droplet microfluidics has grown exponentially in chemistry and biology over the past decades, robust universal platforms for the routine generation and comprehensive analysis of droplet-based artificial cells are still rare. Here we report using microfluidic droplets to reproduce a variety of types of cellular machinery in in vitro artificial cells. In combination with a unique image-based analysis method, the system enables full automation in tracking single droplets with high accuracy, high throughput, and high sensitivity. These powerful performances allow broad applicability evident in three representative droplet-based analytical prototypes that we develop for (i) droplet digital detection, (ii) in vitro transcription and translation reactions, and (iii) spatiotemporal dynamics of cell-cycle oscillations. The capacities of this platform to generate, incubate, track, and analyze individual microdroplets via real-time, long-term imaging unleash its great potential in accelerating cell-free synthetic biology. Moreover, the wide scope covering from digital to analog to morphological detections makes this droplet analysis technique adaptable for many other divergent types of droplet-based chemical and biological assays.
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Affiliation(s)
- Meng Sun
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shiyuan Wang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Gembu Maryu
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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58
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59
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Ahuja K, Rather GM, Lin Z, Sui J, Xie P, Le T, Bertino JR, Javanmard M. Toward point-of-care assessment of patient response: a portable tool for rapidly assessing cancer drug efficacy using multifrequency impedance cytometry and supervised machine learning. MICROSYSTEMS & NANOENGINEERING 2019; 5:34. [PMID: 31645995 PMCID: PMC6799891 DOI: 10.1038/s41378-019-0073-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/31/2019] [Accepted: 03/25/2019] [Indexed: 05/07/2023]
Abstract
We present a novel method to rapidly assess drug efficacy in targeted cancer therapy, where antineoplastic agents are conjugated to antibodies targeting surface markers on tumor cells. We have fabricated and characterized a device capable of rapidly assessing tumor cell sensitivity to drugs using multifrequency impedance spectroscopy in combination with supervised machine learning for enhanced classification accuracy. Currently commercially available devices for the automated analysis of cell viability are based on staining, which fundamentally limits the subsequent characterization of these cells as well as downstream molecular analysis. Our approach requires as little as 20 μL of volume and avoids staining allowing for further downstream molecular analysis. To the best of our knowledge, this manuscript presents the first comprehensive attempt to using high-dimensional data and supervised machine learning, particularly phase change spectra obtained from multi-frequency impedance cytometry as features for the support vector machine classifier, to assess viability of cells without staining or labelling.
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Affiliation(s)
- Karan Ahuja
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Gulam M. Rather
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Zhongtian Lin
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Jianye Sui
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Pengfei Xie
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Tuan Le
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
| | - Joseph R. Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ USA
| | - Mehdi Javanmard
- Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ USA
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60
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Sun M, Li Z, Yang Q. μdroPi: A Hand-Held Microfluidic Droplet Imager and Analyzer Built on Raspberry Pi. JOURNAL OF CHEMICAL EDUCATION 2019; 96:1152-1156. [PMID: 32483390 PMCID: PMC7263740 DOI: 10.1021/acs.jchemed.8b00975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We built a low-cost and hand-held device to image and analyze microfluidic droplets mainly for educational/teaching purposes in laboratory settings of universities. The device was assembled based on a Raspberry Pi with a camera attached on the back and an LCD screen on the top. We evaluated the performance of this device to capture images and videos to visualize high-throughput droplet generation in a microfluidic device. The qualities of imaging resolution and speed were sufficient for us to perform subsequent droplet analysis quantitatively through automatic image possessing. Droplet characteristics including droplet size, volume, and dispersity, as well as droplet intensity, have been measured, showing the potential of this device to analyze droplet-based assays. Most importantly, in addition to learning the knowledge and principles from classroom lectures, students can thus gain practice of using an advanced, state-of-the-art technology in a laboratory course. It will also open up opportunities to train students with skills of interdisciplinary thinking and learning.
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Affiliation(s)
- Meng Sun
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhengda Li
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
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61
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Salomon R, Kaczorowski D, Valdes-Mora F, Nordon RE, Neild A, Farbehi N, Bartonicek N, Gallego-Ortega D. Droplet-based single cell RNAseq tools: a practical guide. LAB ON A CHIP 2019; 19:1706-1727. [PMID: 30997473 DOI: 10.1039/c8lc01239c] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Droplet based scRNA-seq systems such as Drop-seq, inDrop and Chromium 10X have been the catalyst for the wide adoption of high-throughput scRNA-seq technologies in the research laboratory. In order to understand the capabilities of these systems to deeply interrogate biology; here we provide a practical guide through all the steps involved in a typical scRNA-seq experiment. Through comparing and contrasting these three main droplet based systems (and their derivatives), we provide an overview of all critical considerations in obtaining high quality and biologically relevant data. We also discuss the limitations of these systems and how they fit into the emerging field of Genomic Cytometry.
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Affiliation(s)
- Robert Salomon
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.
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62
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Jankowski P, Samborski A, Ostaszewski R, Garstecki P. Evaluation of droplet-based microfluidic platforms as a convenient tool for lipases and esterases assays. Prep Biochem Biotechnol 2019; 49:727-734. [PMID: 31017519 DOI: 10.1080/10826068.2019.1605527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The accurate estimation of kinetic parameters is of fundamental importance for biochemical studies for research and industry. In this paper, we demonstrate the application of a modular microfluidic system for execution of enzyme assays that allow determining the kinetic parameters of the enzymatic reactions such as Vmax - the maximum rate of reaction and KM - the Michaelis constant. For experiments, the fluorogenic carbonate as a probe for a rapid determination of the kinetic parameters of hydrolases, such as lipases and esterases, was used. The microfluidic system together with the method described yields the kinetic constants calculated from the concentration of enzymatic product changes via a Michaelis-Menten model using the Lambert function W(x). This modular microfluidic system was validated on three selected enzymes (hydrolases).
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Affiliation(s)
| | - Adam Samborski
- a Institute of Physical Chemistry , PAS , Warsaw , Poland
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63
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Rapid serial diluting biomicrofluidic provides EC50 in minutes. MICRO AND NANO ENGINEERING 2019. [DOI: 10.1016/j.mne.2019.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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64
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Wei Y, Zhu Y, Fang Q. Nanoliter Quantitative High-Throughput Screening with Large-Scale Tunable Gradients Based on a Microfluidic Droplet Robot under Unilateral Dispersion Mode. Anal Chem 2019; 91:4995-5003. [DOI: 10.1021/acs.analchem.8b04564] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yan Wei
- Institute of Microanalytical Systems, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou 310058, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou 310058, China
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65
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Sun D, Cao F, Cong L, Xu W, Chen Q, Shi W, Xu S. Cellular heterogeneity identified by single-cell alkaline phosphatase (ALP) via a SERRS-microfluidic droplet platform. LAB ON A CHIP 2019; 19:335-342. [PMID: 30566170 DOI: 10.1039/c8lc01006d] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alkaline phosphatase (ALP) is a useful indicator for disease state diagnosis and clinical outcome. Investigation of ALP expression among cells is still challenging since ALP expression in a single cell is too low to be detectable. In our work, an ultrasensitive, high-throughput analytical method was applied for ALP determination in a single cell by using a surface-enhanced resonance Raman scattering (SERRS)-based microfluidic droplet technique. An ALP catalyzed substrate (5-bromo-4-chloro-3-indolyl phosphate, BCIP) was used to evaluate ALP activity in the cell within one droplet. When BCIP was incubated with cells, ALP can catalyze a hydrolysis reaction of colorless BCIP and oxidize the intermediate compound to form blue 5,5'-dibromo-4,4'-dichloro-1H,1H-[2,2']biindolylidene-3,3'-dione (BCI), which is a resonant Raman-active species. The encapsulation of BCI in droplets is favorable for detecting extremely low levels of molecules due to an accumulation effect along with reaction time. The ALP concentration as low as 1.0 × 10-15 M can be successfully detected in a uniform droplet. In addition, cellular heterogeneity profiled by ALP expression on single-cell resolution was monitored with this SERRS-based microfluidic droplet technique. Ultrasensitive determination of ALP secreted from individual cells can help us to understand cell-to-cell heterogeneity.
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Affiliation(s)
- Dan Sun
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, PR China.
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66
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Charon J, Manteca A, Innis CA. Using the Bacterial Ribosome as a Discovery Platform for Peptide-Based Antibiotics. Biochemistry 2019; 58:75-84. [PMID: 30372045 PMCID: PMC7615898 DOI: 10.1021/acs.biochem.8b00927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.
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Affiliation(s)
- Justine Charon
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - Aitor Manteca
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - C. Axel Innis
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
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67
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Svensson CM, Shvydkiv O, Dietrich S, Mahler L, Weber T, Choudhary M, Tovar M, Figge MT, Roth M. Coding of Experimental Conditions in Microfluidic Droplet Assays Using Colored Beads and Machine Learning Supported Image Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1802384. [PMID: 30549235 DOI: 10.1002/smll.201802384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/16/2018] [Indexed: 06/09/2023]
Abstract
To efficiently exploit the potential of several millions of droplets that can be considered as individual bioreactors in microfluidic experiments, methods to encode different experimental conditions in droplets are needed. The approach presented here is based on coencapsulation of colored polystyrene beads with biological samples. The decoding of the droplets, as well as content quantification, are performed by automated analysis of triggered images of individual droplets in-flow using bright-field microscopy. The decoding strategy combines bead classification using a random forest classifier and Bayesian inference to identify different codes and thus experimental conditions. Antibiotic susceptibility testing of nine different antibiotics and the determination of the minimal inhibitory concentration of a specific antibiotic against a laboratory strain of Escherichia coli are presented as a proof-of-principle. It is demonstrated that this method allows successful encoding and decoding of 20 different experimental conditions within a large droplet population of more than 105 droplets per condition. The decoding strategy correctly assigns 99.6% of droplets to the correct condition and a method for the determination of minimal inhibitory concentration using droplet microfluidics is established. The current encoding and decoding pipeline can readily be extended to more codes by adding more bead colors or color combinations.
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Affiliation(s)
- Carl-Magnus Svensson
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Oksana Shvydkiv
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Stefanie Dietrich
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Lisa Mahler
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Thomas Weber
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Mahipal Choudhary
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745, Jena, Germany
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68
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Zhang P, Kaushik A, Hsieh K, Wang TH. Customizing droplet contents and dynamic ranges via integrated programmable picodroplet assembler. MICROSYSTEMS & NANOENGINEERING 2019; 5:22. [PMID: 31636920 PMCID: PMC6799804 DOI: 10.1038/s41378-019-0062-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 05/03/2023]
Abstract
Droplet microfluidic technology is becoming increasingly useful for high-throughput and high-sensitivity detection of biological and biochemical reactions. Most current droplet devices function by passively discretizing a single sample subject to a homogeneous or random reagent/reaction condition into tens of thousands of picoliter-volume droplets for analysis. Despite their apparent advantages in speed and throughput, these droplet devices inherently lack the capability to customize the contents of droplets in order to test a single sample against multiple reagent conditions or multiple samples against multiple reagents. In order to incorporate such combinatorial capability into droplet platforms, we have developed the fully Integrated Programmable Picodroplet Assembler. Our platform is capable of generating customized picoliter-volume droplet groups from nanoliter-volume plugs which are assembled in situ on demand. By employing a combination of microvalves and flow-focusing-based discretization, our platform can be used to precisely control the content and volume of generated nanoliter-volume plugs, and thereafter the content and the effective dynamic range of picoliter-volume droplets. Furthermore, we can use a single integrated device for continuously generating, incubating, and detecting multiple distinct droplet groups. The device successfully marries the precise control and on-demand capability of microvalve-based platforms with the sensitivity and throughput of picoliter droplet platforms in a fully automated monolithic device. The device ultimately will find important applications in single-cell and single-molecule analyses.
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Affiliation(s)
- Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
| | - Aniruddha Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
- Department of Mechanical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218 USA
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69
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Etienne G, Vian A, Biočanin M, Deplancke B, Amstad E. Cross-talk between emulsion drops: how are hydrophilic reagents transported across oil phases? LAB ON A CHIP 2018; 18:3903-3912. [PMID: 30465575 DOI: 10.1039/c8lc01000e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Emulsion drops are frequently used as vessels, for example, to conduct biochemical reactions in small volumes or to perform screening assays at high throughputs while consuming minimal sample volumes. These applications typically require drops that do not allow exchange of reagents such that no cross-contamination occurs. Unfortunately, in many cases, reagents are exchanged between emulsion drops even if they have a low solubility in the surrounding phase, resulting in cross-contaminations. Here, we investigate the mechanism by which hydrophilic reagents are transported across an oil phase using water-oil-water double emulsion drops as a model system. Remarkably, even large objects, including 11 000 base pair double-stranded circular DNA are transported across oil shells. Importantly, this reagent transport, that is to a large extent caused by aqueous drops that spontaneously form at the water-oil interface, is not limited to double emulsions but also occurs between single emulsion drops. We demonstrate that the uncontrolled reagent transport can be decreased by at least an order of magnitude if appropriate surfactants that lower the interfacial tension only moderately are employed or if the shell thickness of double emulsions is decreased to a few hundreds of nanometers.
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Affiliation(s)
- Gianluca Etienne
- Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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70
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Jang MB, Moon T, Choi JH, Chung SH, Ha JW, Lim JM, Lee SK, Yang SM, Youm KH, Shin K, Yi GR. On-demand Microfluidic Manipulation of Thermally Stable Water-in-Perfluorocarbon Emulsions. Macromol Res 2018. [DOI: 10.1007/s13233-018-6144-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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71
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Wang X, Liu Z, Pang Y. Droplet breakup in an asymmetric bifurcation with two angled branches. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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72
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Microfluidics: an Untapped Resource in Viral Diagnostics and Viral Cell Biology. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0105-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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73
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Liu Q, Wang X, Xia T. Creative use of analytical techniques and high-throughput technology to facilitate safety assessment of engineered nanomaterials. Anal Bioanal Chem 2018; 410:6097-6111. [PMID: 30066194 DOI: 10.1007/s00216-018-1289-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/15/2018] [Accepted: 07/23/2018] [Indexed: 12/21/2022]
Abstract
With the rapid development and numerous applications of engineered nanomaterials (ENMs) in science and technology, their impact on environmental health and safety should be considered carefully. This requires an effective platform to investigate the potential adverse effects and hazardous biological outcomes of numerous nanomaterials and their formulations. We consider predictive toxicology a rational approach for this effort, which utilizes mechanism-based in vitro high-throughput screening (HTS) to make predictions on ENMs' adverse outcomes in vivo. Moreover, this approach is able to link the physicochemical properties of ENMs to toxicity that allows the development of structure-activity relationships (SARs). To build this predictive platform, extensive analytical and bioanalytical techniques and tools are required. In this review, we described the predictive toxicology approach and the accompanying analytical and bioanalytical techniques. In addition, we elaborated several successful examples as a result of using the predictive approach.
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Affiliation(s)
- Qi Liu
- Center of Environmental Implications of Nanotechnology (UC CEIN), University of California, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Xiang Wang
- Center of Environmental Implications of Nanotechnology (UC CEIN), University of California, Los Angeles, CA, 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Tian Xia
- Center of Environmental Implications of Nanotechnology (UC CEIN), University of California, Los Angeles, CA, 90095, USA. .,California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA. .,Division of NanoMedicine, Department of Medicine, University of California, 570 Westwood Plaza, Los Angeles, CA, 90095, USA.
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74
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Postek W, Kaminski TS, Garstecki P. A precise and accurate microfluidic droplet dilutor. Analyst 2018; 142:2901-2911. [PMID: 28676870 DOI: 10.1039/c7an00679a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We demonstrate a microfluidic system for the precise (coefficient of variance between repetitions below 4%) and highly accurate (average difference from two-fold dilution below 1%) serial dilution of solutions inside droplets with a volume of ca. 1 μl. The two-fold dilution series can be prepared with the correlation coefficient as high as R2 = 0.999. The technique that we here describe uses hydrodynamic traps to precisely meter every droplet used in subsequent dilutions. We use only one metering trap to meter each and every droplet involved in the process of preparation of the dilution series. This eliminates the error of metering that would arise from the finite fidelity of fabrication of multiple metering traps. Metering every droplet at the same trap provides for high reproducibility of the volumes of the droplets, and thus high reproducibility of dilutions. We also present a device and method to precisely and accurately dilute one substance and simultaneously maintain the concentration of another substance throughout the dilution series without mixing their stock solutions. We compare the here-described precise and accurate dilution systems with a simple microdroplet dilutor that comprises several traps - each trap for a subsequent dilution. We describe the effect of producing more reproducible dilutions in a simple microdroplet dilutor thanks to the application of an alternating electric field.
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Affiliation(s)
- W Postek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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75
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Langer K, Bremond N, Boitard L, Baudry J, Bibette J. Micropipette-powered droplet based microfluidics. BIOMICROFLUIDICS 2018; 12:044106. [PMID: 30034569 PMCID: PMC6039297 DOI: 10.1063/1.5037795] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/26/2018] [Indexed: 05/10/2023]
Abstract
Droplet-based microfluidics, using water-in-oil emulsion droplets as micro-reactors, is becoming a widespread method for performing assays and especially in the cell biology field. Making a simple and highly portable system for creating emulsion droplets would help to continue the popularization of such a technique. Also, the ability to emulsify all the samples would strengthen this compartimenlization technique to handle samples with limited volume. Here, we propose a strategy of droplet formation that combines a classical flow-focusing microfluidic chip, which could be commercially available, with a standard laboratory adjustable micropipette. The micropipette is used as a negative pressure generator for controlling liquid flows. In that way, emulsification does neither require any electrical power supply nor a cumbersome device and functions with small liquid volumes. Droplet formation can be easily and safely performed in places with limited space, opening a wide range of applications especially in biological laboratory environments with higher level of safety regulations, i.e., BSL-3/4. Fortunately, the present methodology that involves small fluid volumes, and thus possible time dependent flow conditions, allows to minimize dead volume while keeping drops' size homogeneous. A physical characterization of droplet production and a model that describes the emulsion features, in terms of drop size and size distribution, are proposed for rationalizing the performances of the micropipette-powered emulsification process.
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Affiliation(s)
- Krzysztof Langer
- Laboratoire Colloïdes et Matériaux Divisés, CNRS UMR 8231, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 rue Vauquelin, F-75005 Paris, France
| | - Nicolas Bremond
- Laboratoire Colloïdes et Matériaux Divisés, CNRS UMR 8231, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 rue Vauquelin, F-75005 Paris, France
| | - Laurent Boitard
- Laboratoire Colloïdes et Matériaux Divisés, CNRS UMR 8231, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 rue Vauquelin, F-75005 Paris, France
| | - Jean Baudry
- Laboratoire Colloïdes et Matériaux Divisés, CNRS UMR 8231, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 rue Vauquelin, F-75005 Paris, France
| | - Jérôme Bibette
- Laboratoire Colloïdes et Matériaux Divisés, CNRS UMR 8231, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 rue Vauquelin, F-75005 Paris, France
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76
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Guan X, Chakrabarti R. Molecular system identification for enzyme directed evolution and design. J Chem Phys 2018; 147:124106. [PMID: 28964026 DOI: 10.1063/1.4996838] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rational design of chemical catalysts requires methods for the measurement of free energy differences in the catalytic mechanism for any given catalyst Hamiltonian. The scope of experimental learning algorithms that can be applied to catalyst design would also be expanded by the availability of such methods. Methods for catalyst characterization typically either estimate apparent kinetic parameters that do not necessarily correspond to free energy differences in the catalytic mechanism or measure individual free energy differences that are not sufficient for establishing the relationship between the potential energy surface and catalytic activity. Moreover, in order to enhance the duty cycle of catalyst design, statistically efficient methods for the estimation of the complete set of free energy differences relevant to the catalytic activity based on high-throughput measurements are preferred. In this paper, we present a theoretical and algorithmic system identification framework for the optimal estimation of free energy differences in solution phase catalysts, with a focus on one- and two-substrate enzymes. This framework, which can be automated using programmable logic, prescribes a choice of feasible experimental measurements and manipulated input variables that identify the complete set of free energy differences relevant to the catalytic activity and minimize the uncertainty in these free energy estimates for each successive Hamiltonian design. The framework also employs decision-theoretic logic to determine when model reduction can be applied to improve the duty cycle of high-throughput catalyst design. Automation of the algorithm using fluidic control systems is proposed, and applications of the framework to the problem of enzyme design are discussed.
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Affiliation(s)
- Xiangying Guan
- Division of Fundamental Research, Chakrabarti Advanced Technology, Mount Laurel, New Jersey 08054, USA
| | - Raj Chakrabarti
- Division of Fundamental Research, Chakrabarti Advanced Technology, Mount Laurel, New Jersey 08054, USA
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77
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Eduati F, Utharala R, Madhavan D, Neumann UP, Longerich T, Cramer T, Saez-Rodriguez J, Merten CA. A microfluidics platform for combinatorial drug screening on cancer biopsies. Nat Commun 2018; 9:2434. [PMID: 29934552 PMCID: PMC6015045 DOI: 10.1038/s41467-018-04919-w] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 06/05/2018] [Indexed: 02/06/2023] Open
Abstract
Screening drugs on patient biopsies from solid tumours has immense potential, but is challenging due to the small amount of available material. To address this, we present here a plug-based microfluidics platform for functional screening of drug combinations. Integrated Braille valves allow changing the plug composition on demand and enable collecting >1200 data points (56 different conditions with at least 20 replicates each) per biopsy. After deriving and validating efficient and specific drug combinations for two genetically different pancreatic cancer cell lines and xenograft mouse models, we additionally screen live cells from human solid tumours with no need for ex vivo culturing steps, and obtain highly specific sensitivity profiles. The entire workflow can be completed within 48 h at assay costs of less than US$ 150 per patient. We believe this can pave the way for rapid determination of optimal personalized cancer therapies.
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Affiliation(s)
- Federica Eduati
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, United Kingdom
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600MB, Eindhoven, The Netherlands
| | - Ramesh Utharala
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dharanija Madhavan
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ulf Peter Neumann
- Department of Surgery, RWTH University Hospital, 52057, Aachen, Germany
- ESCAM - European Surgery Center Aachen Maastricht, Aachen, Germany and Maastricht, The Netherlands
| | - Thomas Longerich
- Institute of Pathology, RWTH University Hospital, 52057, Aachen, Germany
- Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Thorsten Cramer
- ESCAM - European Surgery Center Aachen Maastricht, Aachen, Germany and Maastricht, The Netherlands
- Molecular Tumor Biology, Department Surgery, RWTH University Hospital, 52057, Aachen, Germany
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, United Kingdom.
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52057, Aachen, Germany.
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, BIOQUANT-Center, 69120, Heidelberg, Germany.
| | - Christoph A Merten
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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78
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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.
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79
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Chamoun J, Pattekar A, Afshinmanesh F, Martini J, Recht MI. Optical calorimetry in microfluidic droplets. LAB ON A CHIP 2018; 18:1581-1592. [PMID: 29745386 PMCID: PMC5999407 DOI: 10.1039/c7lc01266g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A novel microfluidic calorimeter that measures the enthalpy change of reactions occurring in 100 μm diameter aqueous droplets in fluoropolymer oil has been developed. The aqueous reactants flow into a microfluidic droplet generation chip in separate fluidic channels, limiting contact between the streams until immediately before they form the droplet. The diffusion-driven mixing of reactants is predominantly restricted to within the droplet. The temperature change in droplets due to the heat of reaction is measured optically by recording the reflectance spectra of encapsulated thermochromic liquid crystals (TLC) that are added to one of the reactant streams. As the droplets travel through the channel, the spectral characteristics of the TLC represent the internal temperature, allowing optical measurement with a precision of ≈6 mK. The microfluidic chip and all fluids are temperature controlled, and the reaction heat within droplets raises their temperature until thermal diffusion dissipates the heat into the surrounding oil and chip walls. Position resolved optical temperature measurement of the droplets allows calculation of the heat of reaction by analyzing the droplet temperature profile over time. Channel dimensions, droplet generation rate, droplet size, reactant stream flows and oil flow rate are carefully balanced to provide rapid diffusional mixing of reactants compared to thermal diffusion, while avoiding thermal "quenching" due to contact between the droplets and the chip walls. Compared to conventional microcalorimetry, which has been used in this work to provide reference measurements, this new continuous flow droplet calorimeter has the potential to perform titrations ≈1000-fold faster while using ≈400-fold less reactants per titration.
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Affiliation(s)
- Jacob Chamoun
- Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, CA 94304, USA.
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80
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Chang JC, Swank Z, Keiser O, Maerkl SJ, Amstad E. Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions. Sci Rep 2018; 8:8143. [PMID: 29802303 PMCID: PMC5970246 DOI: 10.1038/s41598-018-26542-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023] Open
Abstract
Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range and with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable real-time formulation of different reagents using pulse width modulation and consequent encapsulation of the mixed solutions. This device can produce drops from reagent volumes as low as 10 µL with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using drop generators that do not contain valves. We employ this device to monitor the kinetics of the cell-free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device for real-time formulation, we perform DNA titration experiments to test the influence of DNA concentration on the amount of green fluorescence protein produced in double emulsions by a coupled cell-free transcription / translation system.
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Affiliation(s)
- Jui-Chia Chang
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Zoe Swank
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Oliver Keiser
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Esther Amstad
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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81
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82
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Damiati S, Kompella UB, Damiati SA, Kodzius R. Microfluidic Devices for Drug Delivery Systems and Drug Screening. Genes (Basel) 2018; 9:E103. [PMID: 29462948 PMCID: PMC5852599 DOI: 10.3390/genes9020103] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Microfluidic devices present unique advantages for the development of efficient drug carrier particles, cell-free protein synthesis systems, and rapid techniques for direct drug screening. Compared to bulk methods, by efficiently controlling the geometries of the fabricated chip and the flow rates of multiphase fluids, microfluidic technology enables the generation of highly stable, uniform, monodispersed particles with higher encapsulation efficiency. Since the existing preclinical models are inefficient drug screens for predicting clinical outcomes, microfluidic platforms might offer a more rapid and cost-effective alternative. Compared to 2D cell culture systems and in vivo animal models, microfluidic 3D platforms mimic the in vivo cell systems in a simple, inexpensive manner, which allows high throughput and multiplexed drug screening at the cell, organ, and whole-body levels. In this review, the generation of appropriate drug or gene carriers including different particle types using different configurations of microfluidic devices is highlighted. Additionally, this paper discusses the emergence of fabricated microfluidic cell-free protein synthesis systems for potential use at point of care as well as cell-, organ-, and human-on-a-chip models as smart, sensitive, and reproducible platforms, allowing the investigation of the effects of drugs under conditions imitating the biological system.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Uday B Kompella
- Department of Pharmaceutical Sciences, Ophthalmology, and Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Safa A Damiati
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Materials Genome Institute, Shanghai University, Shanghai 200444, China.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
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83
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Campana O, Wlodkowic D. Ecotoxicology Goes on a Chip: Embracing Miniaturized Bioanalysis in Aquatic Risk Assessment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:932-946. [PMID: 29284083 DOI: 10.1021/acs.est.7b03370] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Biological and environmental sciences are, more than ever, becoming highly dependent on technological and multidisciplinary approaches that warrant advanced analytical capabilities. Microfluidic lab-on-a-chip technologies are perhaps one the most groundbreaking offshoots of bioengineering, enabling design of an entirely new generation of bioanalytical instrumentation. They represent a unique approach to combine microscale engineering and physics with specific biological questions, providing technological advances that allow for fundamentally new capabilities in the spatiotemporal analysis of molecules, cells, tissues, and even small metazoan organisms. While these miniaturized analytical technologies experience an explosive growth worldwide, with a substantial promise of a direct impact on biosciences, it seems that lab-on-a-chip systems have so far escaped the attention of aquatic ecotoxicologists. In this Critical Review, potential applications of the currently existing and emerging chip-based technologies for aquatic ecotoxicology and water quality monitoring are highlighted. We also offer suggestions on how aquatic ecotoxicology can benefit from adoption of microfluidic lab-on-a-chip devices for accelerated bioanalysis.
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Affiliation(s)
- Olivia Campana
- Instituto de Ciencias Marinas de Andalucía, CSIC , Puerto Real, 11519, Spain
| | - Donald Wlodkowic
- School of Science, RMIT University , Melbourne, Victoria 3083, Australia
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84
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Zdrali E, Chen Y, Okur HI, Wilkins DM, Roke S. The Molecular Mechanism of Nanodroplet Stability. ACS NANO 2017; 11:12111-12120. [PMID: 29224343 DOI: 10.1021/acsnano.7b05100] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mixtures of nano- and microscopic oil droplets in water have recently been rediscovered as miniature reaction vessels in microfluidic environments and are important constituents of many environmental systems, food, personal care, and medical products. The oil nanodroplet/water interface stabilized by surfactants determines the physicochemical properties of the droplets. Surfactants are thought to stabilize nanodroplets by forming densely packed monolayers that shield the oil phase from the water. This idea has been inferred from droplet stability measurements in combination with molecular structural data obtained from extended planar interfaces. Here, we present a molecular level investigation of the surface structure and stability of nanodroplets and show that the surface structure of nanodroplets is significantly different from that of extended planar interfaces. Charged surfactants form monolayers that are more than 1 order of magnitude more dilute than geometrically packed ones, and there is no experimental correlation between stability and surfactant surface density. Moreover, dilute negatively charged surfactant monolayers produce more stable nanodroplets than dilute positively charged and dense geometrically packed neutral surfactant monolayers. Droplet stability is found to depend on the relative cooperativity between charge-charge, charge-dipole, and hydrogen-bonding interactions. The difference between extended planar interfaces and nanoscale interfaces stems from a difference in the thermally averaged total charge-charge interactions in the two systems. Low dielectric oil droplets with a size smaller than the Debye length in oil permit repulsive interactions between like charges from opposing interfaces in small droplets. This behavior is generic and extends up to the micrometer length scale.
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Affiliation(s)
- Evangelia Zdrali
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Yixing Chen
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Halil I Okur
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - David M Wilkins
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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85
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Song W, Lin G, Ge J, Fassbender J, Makarov D. Encoding Microreactors with Droplet Chains in Microfluidics. ACS Sens 2017; 2:1839-1846. [PMID: 29183119 DOI: 10.1021/acssensors.7b00700] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Droplet-based high throughput biomolecular screening and combinatorial synthesis entail a viable indexing strategy to be developed for the identification of each microreactor. Here, we propose a novel indexing scheme based on the generation of droplet sequences on demand to form unique encoding droplet chains in fluidic networks. These codes are represented by multiunit and multilevel droplets packages, with each code unit possessing several distinct signal levels, potentially allowing large encoding capacity. For proof of concept, we use magnetic nanoparticles as the encoding material and a giant magnetoresistance (GMR) sensor-based active sorting system supplemented with an optical detector to generate and decode the sequence of one exemplar sample droplet reactor and a 4-unit quaternary magnetic code. The indexing capacity offered by 4-unit multilevel codes with this indexing strategy is estimated to exceed 104, which holds great promise for large-scale droplet-based screening and synthesis.
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Affiliation(s)
- Wenya Song
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
| | - Gungun Lin
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
- University of Technology Sydney, Institute for Biomedical Materials
and Devices (IBMD), School of Mathematical and Physical Sciences, Ultimo, NSW 2007, Australia
| | - Jin Ge
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
| | - Jürgen Fassbender
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
- Technische Universität Dresden, Zellescher Weg 16, 01069 Dresden, Germany
| | - Denys Makarov
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
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86
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Microfluidics for Combating Antimicrobial Resistance. Trends Biotechnol 2017; 35:1129-1139. [DOI: 10.1016/j.tibtech.2017.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 01/09/2023]
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87
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Cochrane WG, Hackler AL, Cavett VJ, Price AK, Paegel BM. Integrated, Continuous Emulsion Creamer. Anal Chem 2017; 89:13227-13234. [PMID: 29124927 DOI: 10.1021/acs.analchem.7b03070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Automated and reproducible sample handling is a key requirement for high-throughput compound screening and currently demands heavy reliance on expensive robotics in screening centers. Integrated droplet microfluidic screening processors are poised to replace robotic automation by miniaturizing biochemical reactions to the droplet scale. These processors must generate, incubate, and sort droplets for continuous droplet screening, passively handling millions of droplets with complete uniformity, especially during the key step of sample incubation. Here, we disclose an integrated microfluidic emulsion creamer that packs ("creams") assay droplets by draining away excess oil through microfabricated drain channels. The drained oil coflows with creamed emulsion and then reintroduces the oil to disperse the droplets at the circuit terminus for analysis. Creamed emulsion assay incubation time dispersion was 1.7%, 3-fold less than other reported incubators. The integrated, continuous emulsion creamer (ICEcreamer) was used to miniaturize and optimize measurements of various enzymatic activities (phosphodiesterase, kinase, bacterial translation) under multiple- and single-turnover conditions. Combining the ICEcreamer with current integrated microfluidic DNA-encoded library bead processors eliminates potentially cumbersome instrumentation engineering challenges and is compatible with assays of diverse target class activities commonly investigated in drug discovery.
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Affiliation(s)
- Wesley G Cochrane
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Amber L Hackler
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Valerie J Cavett
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander K Price
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Doctoral Program in the Chemical and Biological Sciences and ‡Department of Chemistry, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
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88
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Gerhardt RF, Peretzki AJ, Piendl SK, Belder D. Seamless Combination of High-Pressure Chip-HPLC and Droplet Microfluidics on an Integrated Microfluidic Glass Chip. Anal Chem 2017; 89:13030-13037. [DOI: 10.1021/acs.analchem.7b04331] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Renata F. Gerhardt
- Institute of Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Andrea J. Peretzki
- Institute of Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Sebastian K. Piendl
- Institute of Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
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89
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Skilitsi AI, Turko T, Cianfarani D, Barre S, Uhring W, Hassiepen U, Léonard J. Towards sensitive, high-throughput, biomolecular assays based on fluorescence lifetime. Methods Appl Fluoresc 2017; 5:034002. [PMID: 28699919 DOI: 10.1088/2050-6120/aa7f66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing time-correlated single photon counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by time-correlated single photon counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second.
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Affiliation(s)
- Anastasia Ioanna Skilitsi
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67000 Strasbourg, France
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90
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Prastowo A, Feuerborn A, Cook PR, Walsh EJ. Biocompatibility of fluids for multiphase drops-in-drops microfluidics. Biomed Microdevices 2017; 18:114. [PMID: 27921279 PMCID: PMC5138278 DOI: 10.1007/s10544-016-0137-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This paper addresses the biocompatibility of fluids and surfactants in the context of microfluidics and more specifically in a drops-in-drops system for mammalian cell based drug screening. In the drops-in-drops approach, three immiscible fluids are used to manipulate the flow of aqueous microliter-sized drops; it enables merging of drops containing cells with drops containing drugs within a Teflon tube. Preliminary tests showed that a commonly-used fluid and surfactant combination resulted in significant variability in gene expression levels in Jurkat cells after exposure to a drug for four hours. This result led to further investigations of potential fluid and surfactant combinations that can be used in microfluidic systems for medium to long-term drug screening. Results herein identify a fluid combination, HFE-7500 and 5-cSt silicone oil + 0.25% Abil EM180, which enabled the drops-in-drops approach; this combination also allowed gene expression at normal levels comparable with the conventional drug screening in both magnitude and variability.
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Affiliation(s)
- Aishah Prastowo
- Osney Thermo-Fluids Laboratory, Department of Engineering Science, University of Oxford, Osney Mead, Oxford, OX2 0ES, UK
| | - Alexander Feuerborn
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Edmond J Walsh
- Osney Thermo-Fluids Laboratory, Department of Engineering Science, University of Oxford, Osney Mead, Oxford, OX2 0ES, UK.
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91
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Baccouche A, Okumura S, Sieskind R, Henry E, Aubert-Kato N, Bredeche N, Bartolo JF, Taly V, Rondelez Y, Fujii T, Genot AJ. Massively parallel and multiparameter titration of biochemical assays with droplet microfluidics. Nat Protoc 2017; 12:1912-1932. [PMID: 28837132 DOI: 10.1038/nprot.2017.092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biochemical systems in which multiple components take part in a given reaction are of increasing interest. Because the interactions between these different components are complex and difficult to predict from basic reaction kinetics, it is important to test for the effect of variations in the concentration for each reagent in a combinatorial manner. For example, in PCR, an increase in the concentration of primers initially increases template amplification, but large amounts of primers result in primer-dimer by-products that inhibit the amplification of the template. Manual titration of biochemical mixtures rapidly becomes costly and laborious, forcing scientists to settle for suboptimal concentrations. Here we present a droplet-based microfluidics platform for mapping of the concentration space of up to three reaction components followed by detection with a fluorescent readout. The concentration of each reaction component is read through its internal standard (barcode), which is fluorescent but chemically orthogonal. We describe in detail the workflow, which comprises the following: (i) production of the microfluidics chips, (ii) preparation of the biochemical mixes, (iii) their mixing and compartmentalization into water-in-oil emulsion droplets via microfluidics, (iv) incubation and imaging of the fluorescent barcode and reporter signals by fluorescence microscopy and (v) image processing and data analysis. We also provide recommendations for choosing the appropriate fluorescent markers, programming the pressure profiles and analyzing the generated data. Overall, this platform allows a researcher with a few weeks of training to acquire ∼10,000 data points (in a 1D, 2D or 3D concentration space) over the course of a day from as little as 100-1,000 μl of reaction mix.
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Affiliation(s)
- Alexandre Baccouche
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Earth Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Shu Okumura
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,CIBIS, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Rémi Sieskind
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Elia Henry
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Nathanaël Aubert-Kato
- Earth Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Information Science, Ochanomizu University, Tokyo, Japan.,Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institute of Intelligent Systems and Robotics (ISIR), Paris, France
| | - Nicolas Bredeche
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institute of Intelligent Systems and Robotics (ISIR), Paris, France
| | | | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Paris Descartes University, Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Yannick Rondelez
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Teruo Fujii
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan.,CIBIS, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, The University of Tokyo, Tokyo, Japan
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92
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Drug screening of cancer cell lines and human primary tumors using droplet microfluidics. Sci Rep 2017; 7:9109. [PMID: 28831060 PMCID: PMC5567315 DOI: 10.1038/s41598-017-08831-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/19/2017] [Indexed: 01/23/2023] Open
Abstract
Precision Medicine in Oncology requires tailoring of therapeutic strategies to individual cancer patients. Due to the limited quantity of tumor samples, this proves to be difficult, especially for early stage cancer patients whose tumors are small. In this study, we exploited a 2.4 × 2.4 centimeters polydimethylsiloxane (PDMS) based microfluidic chip which employed droplet microfluidics to conduct drug screens against suspended and adherent cancer cell lines, as well as cells dissociated from primary tumor of human patients. Single cells were dispersed in aqueous droplets and imaged within 24 hours of drug treatment to assess cell viability by ethidium homodimer 1 staining. Our results showed that 5 conditions could be screened for every 80,000 cells in one channel on our chip under current circumstances. Additionally, screening conditions have been adapted to both suspended and adherent cancer cells, giving versatility to potentially all types of cancers. Hence, this study provides a powerful tool for rapid, low-input drug screening of primary cancers within 24 hours after tumor resection from cancer patients. This paves the way for further technological advancement to cutting down sample size and increasing drug screening throughput in advent to personalized cancer therapy.
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93
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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.
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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;
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94
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Abstract
Droplet microfluidics generates and manipulates discrete droplets through immiscible multiphase flows inside microchannels. Due to its remarkable advantages, droplet microfluidics bears significant value in an extremely wide range of area. In this review, we provide a comprehensive and in-depth insight into droplet microfluidics, covering fundamental research from microfluidic chip fabrication and droplet generation to the applications of droplets in bio(chemical) analysis and materials generation. The purpose of this review is to convey the fundamentals of droplet microfluidics, a critical analysis on its current status and challenges, and opinions on its future development. We believe this review will promote communications among biology, chemistry, physics, and materials science.
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Affiliation(s)
- Luoran Shang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Yao Cheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - Yuanjin Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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95
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Chen X, Ren CL. Experimental study on droplet generation in flow focusing devices considering a stratified flow with viscosity contrast. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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96
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Ochoa A, Álvarez-Bohórquez E, Castillero E, Olguin LF. Detection of Enzyme Inhibitors in Crude Natural Extracts Using Droplet-Based Microfluidics Coupled to HPLC. Anal Chem 2017; 89:4889-4896. [DOI: 10.1021/acs.analchem.6b04988] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Abraham Ochoa
- Laboratorio de Biofisicoquímica,
Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Enrique Álvarez-Bohórquez
- Laboratorio de Biofisicoquímica,
Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Eduardo Castillero
- Laboratorio de Biofisicoquímica,
Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Luis F. Olguin
- Laboratorio de Biofisicoquímica,
Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
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97
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Wang H, Chen B, He M, Hu B. A Facile Droplet-Chip-Time-Resolved Inductively Coupled Plasma Mass Spectrometry Online System for Determination of Zinc in Single Cell. Anal Chem 2017; 89:4931-4938. [DOI: 10.1021/acs.analchem.7b00134] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Han Wang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), Department
of Chemistry, Wuhan University, Wuhan 430072, China
| | - Beibei Chen
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), Department
of Chemistry, Wuhan University, Wuhan 430072, China
| | - Man He
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), Department
of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bin Hu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), Department
of Chemistry, Wuhan University, Wuhan 430072, China
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98
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Frenzel D, Merten CA. Microfluidic train station: highly robust and multiplexable sorting of droplets on electric rails. LAB ON A CHIP 2017; 17:1024-1030. [PMID: 28232987 PMCID: PMC5544107 DOI: 10.1039/c6lc01544a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has become a widely used technique for high-throughput screening applications. However, existing methods are very sensitive to fluctuating flow rates at the sorting junction, which can be caused by the pulsing effects of mechanical pumps, droplet aggregates or the accumulation of precipitates during lengthy biological screening applications. Furthermore, existing sorting devices allow only 2-way sorting. We present here a dielectrophoretic sorting system in which the droplets are sorted along multiple electrode pairs that run parallel to the channels. This enables highly reliable sorting (no errors were detected for more than 2000 sorting events) even when inverting the relative flow rates at a 2-way sorting junction from 80 : 20 to 20 : 80. Furthermore, our toolbox is scalable: we demonstrate on the example of a triple-colour sorting experiment with a total of four decoupled electrodes that multi-way sorting is feasible.
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Affiliation(s)
- Daniel Frenzel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Christoph A Merten
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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99
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Qu X, Zhang H, Chen H, Aldalbahi A, Li L, Tian Y, Weitz DA, Pei H. Convection-Driven Pull-Down Assays in Nanoliter Droplets Using Scaffolded Aptamers. Anal Chem 2017; 89:3468-3473. [PMID: 28207249 DOI: 10.1021/acs.analchem.6b04475] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing the contents of droplets with nano- or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull down. The convective flux allows complete reaction in <5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of the stationary case). This established DNaPull assay can serve as a rapid and sensitive analytical platform for analyzing a variety of bioactive molecules, including small molecules [ATP, limit of detecton (LOD) of 1 μM], a drug (cocaine, LOD of 1 μM), and a biomarker (thrombin, LOD of 0.1 nM). Significantly, the designed microfluidic device compartmentalizes live cells into nanoliter-sized droplets to present single-cell samples. As a proof of concept, we demonstrated that cellular molecules (ATP) from a discrete number of HNE1 cells (zero to five cells) lysed inside nanoliter-sized droplets can be analyzed using our DNaPull assay, in which the intracellular ATP level was estimated to be ∼3.4 mM. Given the rapid assay feature and single-cell sample analysis ability, we believe that our analytical platform of convection-driven DNaPull in a glass capillary can provide a new paradigm in biosensor design and will be valuable for single-cell analysis.
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Affiliation(s)
- Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China.,Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Hongbo Zhang
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States.,Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Hong Chen
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, P. R. China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - David A Weitz
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China
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100
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Droplet Microfluidics Approach for Single-DNA Molecule Amplification and Condensation into DNA-Magnesium-Pyrophosphate Particles. MICROMACHINES 2017. [PMCID: PMC6189807 DOI: 10.3390/mi8020062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein expression in vitro has broad applications in directed evolution, synthetic biology, proteomics and drug screening. However, most of the in vitro expression systems rely on relatively high DNA template concentrations to obtain sufficient amounts of proteins, making it harder to perform in vitro screens on gene libraries. Here, we report a technique for the generation of condensed DNA particles that can serve as efficient templates for in vitro gene expression. We apply droplet microfluidics to encapsulate single-DNA molecules in 3-picoliter (pL) volume droplets and convert them into 1 μm-sized DNA particles by the multiple displacement amplification reaction driven by phi29 DNA polymerase. In the presence of magnesium ions and inorganic pyrophosphate, the amplified DNA condensed into the crystalline-like particles, making it possible to purify them from the reaction mix by simple centrifugation. Using purified DNA particles, we performed an in vitro transcription-translation reaction and successfully expressed complex enzyme β-galactosidase in droplets and in the 384-well format. The yield of protein obtained from DNA particles was significantly higher than from the corresponding amount of free DNA templates, thus opening new possibilities for high throughput screening applications.
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