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Luo Y, Hu Q, Yu Y, Lyu W, Shen F. Experimental investigation of confinement effect in single molecule amplification via real-time digital PCR on a multivolume droplet array SlipChip. Anal Chim Acta 2024; 1304:342541. [PMID: 38637051 DOI: 10.1016/j.aca.2024.342541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Digital polymerase chain reaction (digital PCR) is an important quantitative nucleic acid analysis method in both life science research and clinical diagnostics. One important hypothesis is that by physically constraining a single nucleic acid molecule in a small volume, the relative concentration can be increased therefore further improving the analysis performance, and this is commonly defined as the confinement effect in digital PCR. However, experimental investigation of this confinement effect can be challenging since it requires a microfluidic device that can generate partitions of different volumes and an instrument that can monitor the kinetics of amplification. (96). RESULTS Here, we developed a real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip) that can generate droplet of 125 nL, 25 nL, 5 nL, and 1 nL by a simple "load-slip" operation. In the digital region, by reducing the volume, the relative concentration is increased, the amplification kinetic can be accelerated, and the time to reach the fluorescence threshold, or Cq value, can be reduced. When the copy number per well is much higher than one, the relative concentration is independent of the partition volume, thus the amplification kinetics are similar in different volume partitions. This system is not limited to studying the kinetics of digital nucleic acid amplification, it can also extend the dynamic range of the digital nucleic acid analysis by additional three orders of magnitude by combining a digital and an analog quantification algorithm. (140). SIGNIFICANCE In this study, we experimentally investigated for the first time the confinement effect in the community of digital PCR via a new real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip). And a wider dynamic range of quantification methods compared to conventional digital PCR was validated by this system. This system provides emerging opportunities for life science research and clinical diagnostics. (63).
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Affiliation(s)
- Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China.
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2
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Hosokawa K, Ohmori H. Digital PCR using a simple PDMS microfluidic chip and standard laboratory equipment. ANAL SCI 2023; 39:2067-2074. [PMID: 37710081 DOI: 10.1007/s44211-023-00425-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
Digital PCR (dPCR) enables sensitive and precise quantification of template nucleic acid without calibration. However, dPCR is not yet in widespread use, probably due to the need for expensive specialized instruments. In this paper, we describe a dPCR system using a simple microfluidic chip and common laboratory tools. The microfluidic chip consists of two parts: a PDMS part with 24,840 × 0.25 nL microwells and a PDMS-coated flat glass plate. Human RNase P gene was adopted as the model template. Commercial products of human genomic DNA and real-time PCR reagents were mixed to make a PCR mixture. The PCR mixture was confined to the microwells by the PDMS degas-driven liquid control technique. The thermal cycling was performed on a common well-type thermal cycler with a minor modification. During the thermal cycling, evaporation of the PCR mixture was prevented with a handmade water holder. In the fluorescence image, bright (positive) microwells and dim (negative) ones were clearly discriminated. The number of the positive microwells was counted using software, and was used for estimation of the template concentration in the sample based on the theory of the Poisson distribution. The estimated concentrations well agreed with the input template concentrations in the range from 1.32 copies/µL to 13 200 copies/µL. The techniques presented in this paper will pave the way for facile dPCR in a broad range of laboratories without the need for expensive instruments.
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Affiliation(s)
- Kazuo Hosokawa
- Materials Fabrication Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Hitoshi Ohmori
- Materials Fabrication Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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3
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Budassi J, Cho N, Del Valle A, Sokolov J. Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules. PLoS One 2023; 18:e0250054. [PMID: 37672538 PMCID: PMC10482287 DOI: 10.1371/journal.pone.0250054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/24/2023] [Indexed: 09/08/2023] Open
Abstract
We describe a method for fragmenting, in-situ, surface-adsorbed and immobilized DNAs on polymethylmethacrylate(PMMA)-coated silicon substrates using microfluidic delivery of the cutting enzyme DNase I. Soft lithography is used to produce silicone elastomer (Sylgard 184) gratings which form microfluidic channels for delivery of the enzyme. Bovine serum albumin (BSA) is used to reduce DNase I adsorption to the walls of the microchannels and enable diffusion of the cutting enzyme to a distance of 10mm. Due to the DNAs being immobilized, the fragment order is maintained on the surface. Possible methods of preserving the order for application to sequencing are discussed.
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Affiliation(s)
- Julia Budassi
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - NaHyun Cho
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - Anthony Del Valle
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York, United States of America
| | - Jonathan Sokolov
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
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Nouri R, Jiang Y, Politza AJ, Liu T, Greene WH, Zhu Y, Nunez JJ, Lian X, Guan W. STAMP-Based Digital CRISPR-Cas13a for Amplification-Free Quantification of HIV-1 Plasma Viral Loads. ACS NANO 2023; 17:10701-10712. [PMID: 37252938 PMCID: PMC11240847 DOI: 10.1021/acsnano.3c01917] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Quantification of HIV RNA in plasma is critical for identifying the disease progression and monitoring the effectiveness of antiretroviral therapy. While RT-qPCR has been the gold standard for HIV viral load quantification, digital assays could provide an alternative calibration-free absolute quantification method. Here, we reported a Self-digitization Through Automated Membrane-based Partitioning (STAMP) method to digitalize the CRISPR-Cas13 assay (dCRISPR) for amplification-free and absolute quantification of HIV-1 viral RNAs. The HIV-1 Cas13 assay was designed, validated, and optimized. We evaluated the analytical performances with synthetic RNAs. With a membrane that partitions ∼100 nL of reaction mixture (effectively containing 10 nL of input RNA sample), we showed that RNA samples spanning 4 orders of dynamic range between 1 fM (∼6 RNAs) to 10 pM (∼60k RNAs) could be quantified as fast as 30 min. We also examined the end-to-end performance from RNA extraction to STAMP-dCRISPR quantification using 140 μL of both spiked and clinical plasma samples. We demonstrated that the device has a detection limit of approximately 2000 copies/mL and can resolve a viral load change of 3571 copies/mL (equivalent to 3 RNAs in a single membrane) with 90% confidence. Finally, we evaluated the device using 140 μL of 20 patient plasma samples (10 positives and 10 negatives) and benchmarked the performance with RT-PCR. The STAMP-dCRISPR results agree very well with RT-PCR for all negative and high positive samples with Ct < 32. However, the STAMP-dCRISPR is limited in detecting low positive samples with Ct > 32 due to the subsampling errors. Our results demonstrated a digital Cas13 platform that could offer an accessible amplification-free quantification of viral RNAs. By further addressing the subsampling issue with approaches such as preconcentration, this platform could be further exploited for quantitatively determining viral load for an array of infectious diseases.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Wallace H Greene
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Yusheng Zhu
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Jonathan J Nunez
- Department of Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, United States
| | - Xiaojun Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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5
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Luo Y, Cao Z, Liu Y, Zhang R, Yang S, Wang N, Shi Q, Li J, Dong S, Fan C, Zhao J. The emerging landscape of microfluidic applications in DNA data storage. LAB ON A CHIP 2023; 23:1981-2004. [PMID: 36946437 DOI: 10.1039/d2lc00972b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA has been considered a promising alternative to the current solid-state devices for digital information storage. The past decade has witnessed tremendous progress in the field of DNA data storage contributed by researchers from various disciplines. However, the current development status of DNA storage is still far from practical use, mainly due to its high material cost and time consumption for data reading/writing, as well as the lack of a comprehensive, automated, and integrated system. Microfluidics, being capable of handling and processing micro-scale fluid samples in a massively paralleled and highly integrated manner, has gradually been recognized as a promising candidate for addressing the aforementioned issues. In this review, we provide a discussion on recent efforts of applying microfluidics to advance the development of DNA data storage. Moreover, to showcase the tremendous potential that microfluidics can contribute to this field, we will further highlight the recent advancements of applying microfluidics to the key functional modules within the DNA data storage workflow. Finally, we share our perspectives on future directions for how to continue the infusion of microfluidics with DNA data storage and how to advance toward a truly integrated system and reach real-life applications.
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Affiliation(s)
- Yuan Luo
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shijia Yang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Wang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyuan Shi
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P.R. China
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6
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Abstract
Droplet digital polymerase chain reaction (ddPCR) is a new quantitative PCR method based on water-oil emulsion droplet technology. ddPCR enables highly sensitive and accurate quantification of nucleic acid molecules, especially when their copy numbers are low. In ddPCR, a sample is fractionated into ~20,000 droplets, and every nanoliter-sized droplet undergoes PCR amplification of the target molecule. The fluorescence signals of droplets are then recorded by an automated droplet reader. Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are ubiquitously expressed in animals and plants. CircRNAs are promising as biomarkers for cancer diagnosis and prognosis and as therapeutic targets or agents to inhibit oncogenic microRNAs or proteins (Kristensen LS, Jakobsen T, Hager H, Kjems J, Nat Rev Clin Oncol 19:188-206, 2022). In this chapter, the procedures for the quantitation of a circRNA in single pancreatic cancer cells using ddPCR are described.
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Affiliation(s)
- Jiayi Peng
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Feng Li
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Xiangdong Xu
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Shen Hu
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.
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7
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Chen S, Sun Y, Fan F, Chen S, Zhang Y, Zhang Y, Meng X, Lin JM. Present status of microfluidic PCR chip in nucleic acid detection and future perspective. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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8
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Chen X, Song Q, Zhang B, Gao Y, Lou K, Liu Y, Wen W. A Rapid Digital PCR System with a Pressurized Thermal Cycler. MICROMACHINES 2021; 12:mi12121562. [PMID: 34945412 PMCID: PMC8708658 DOI: 10.3390/mi12121562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
We designed a silicon-based fast-generated static droplets array (SDA) chip and developed a rapid digital polymerase chain reaction (dPCR) detection platform that is easy to load samples for fluorescence monitoring. By using the direct scraping method for sample loading, a droplet array of 2704 microwells with each volume of about 0.785 nL can be easily realized. It was determined that the sample loading time was less than 10 s with very simple and efficient characteristics. In this platform, a pressurized thermal cycling device was first used to solve the evaporation problem usually encountered for dPCR experiments, which is critical to ensuring the successful amplification of templates at the nanoliter scale. We used a gradient dilution of the hepatitis B virus (HBV) plasmid as the target DNA for a dPCR reaction to test the feasibility of the dPCR chip. Our experimental results demonstrated that the dPCR chip could be used to quantitatively detect DNA molecules. Furthermore, the platform can measure the fluorescence intensity in real-time. To test the accuracy of the digital PCR system, we chose three-channel silicon-based chips to operate real-time fluorescent PCR experiments on this platform.
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Affiliation(s)
- Xuee Chen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; (X.C.); (Q.S.)
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; (X.C.); (Q.S.)
- Guangzhou HKUST Fok Ying Tung Research Institute, Guangzhou 511458, China
| | - Beini Zhang
- Advanced Materials Thrust, Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong;
| | - Yibo Gao
- Zhuhai Shineway Biotech Co., Ltd., Zhuhai 519000, China;
| | - Kai Lou
- Guangzhou Kayja-Optics Technology Co., Ltd., Guangzhou 511458, China;
| | - Yiteng Liu
- Earth, Ocean and Atmospheric Sciences Thrust, Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong;
| | - Weijia Wen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; (X.C.); (Q.S.)
- Advanced Materials Thrust, Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong;
- Correspondence: ; Tel.: +852-2358-7979
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9
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Zhang W, Zheng K, Ye Y, Ji J, Cheng X, He S. Pipette-Tip-Enabled Digital Nucleic Acid Analyzer for COVID-19 Testing with Isothermal Amplification. Anal Chem 2021; 93:15288-15294. [PMID: 34735121 DOI: 10.1021/acs.analchem.1c02414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Herein, a pipette-tip-enabled digital nucleic acid analyzer for high-performance COVID-19 testing is demonstrated. This is achieved by digital loop-mediated isothermal amplification (digital LAMP or dLAMP) using common laboratory equipment and materials. It is shown that simply fixing a glass capillary inside conventional pipette tips enables the generation of monodisperse, water-in-oil microdroplets with benchtop centrifugation. It is shown that using LAMP, the ORF1a/b gene, a standard test region for COVID-19 screening, can be amplified without a thermal cycler. The amplification allows counting of fluorescent microdroplets so that Poisson analysis can be performed to allow quantification with a limit of detection that is 1 order of magnitude better than those of nondigital techniques and comparable to those of commercial dLAMP platforms. It is envisioned that this work will inspire studies on ultrasensitive digital nucleic acid analyzers demanding both sensitivity and accessibility, which is pivotal to their large-scale applications.
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Affiliation(s)
- Wenyao Zhang
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China
| | - Kaixin Zheng
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China
| | - Yang Ye
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China.,Ningbo Research Institute, Ningbo 310050, China.,ZJU-TU/e Joint Research Institute of Design, Optoelectronic and Sensing, Hangzhou 310052, China
| | - Jiali Ji
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China
| | - Xiaoyu Cheng
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China.,Ningbo Research Institute, Ningbo 310050, China.,ZJU-TU/e Joint Research Institute of Design, Optoelectronic and Sensing, Hangzhou 310052, China
| | - Sailing He
- National Engineering Research Center for Optical Instruments, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310052, China.,Ningbo Research Institute, Ningbo 310050, China.,ZJU-TU/e Joint Research Institute of Design, Optoelectronic and Sensing, Hangzhou 310052, China
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10
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Cao L, Guo X, Mao P, Ren Y, Li Z, You M, Hu J, Tian M, Yao C, Li F, Xu F. A Portable Digital Loop-Mediated Isothermal Amplification Platform Based on Microgel Array and Hand-Held Reader. ACS Sens 2021; 6:3564-3574. [PMID: 34606243 DOI: 10.1021/acssensors.1c00603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Digital polymerase chain reaction (dPCR) has found widespread applications in molecular diagnosis of various diseases owing to its sensitive single-molecule detection capability. However, the existing dPCR platforms rely on the auxiliary procedure to disperse DNA samples, which needs complicated operation, expensive apparatus, and consumables. Besides, the complex and costly dPCR readers also impede the applications of dPCR for point-of-care testing (POCT). Herein, we developed a portable digital loop-mediated isothermal amplification (dLAMP) platform, integrating a microscale hydrogel (microgel) array chip for sample partition, a miniaturized heater for DNA amplification, and a hand-held reader for digital readout. In the platform, the chip with thousands of isolated microgels holds the capability of self-absorption and partition of DNA samples, thus avoiding auxiliary equipment and professional personnel operations. Using the integrated dLAMP platform, λDNA templates have been quantified with a good linear detection range of 2-1000 copies/μL and a detection limit of 1 copy/μL. As a demonstration, the epidermal growth factor receptor L858R gene mutation, a crucial factor for the susceptibility of the tyrosine kinase inhibitor in non-small-cell lung cancer treatment, has been accurately identified by the dLAMP platform with a spiked plasma sample. This work shows that the developed dLAMP platform provides a low-cost, facile, and user-friendly solution for the absolute quantification of DNA, showing great potential for the POCT of nucleic acids.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaojin Guo
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
- Department of Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Ping Mao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yulin Ren
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Jie Hu
- Suzhou DiYinAn Biotechnology Company Ltd., Suzhou 215000, China
| | - Miao Tian
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Fei Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
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11
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Lyu W, Zhang J, Yu Y, Xu L, Shen F. Slip formation of a high-density droplet array for nucleic acid quantification by digital LAMP with a random-access system. LAB ON A CHIP 2021; 21:3086-3093. [PMID: 34160518 DOI: 10.1039/d1lc00361e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Digital nucleic acid analysis (digital NAA) is an important tool for the precise quantification of nucleic acids. Various microfluidic-based approaches for digital NAA have been developed, but most methods require complex auxiliary control instruments, cumbersome device fabrication, or inconvenient preparation processes. A SlipChip is a microfluidic device that can generate and manipulate liquid partitions through simple movements of two microfluidic plates in close contact. However, the traditional SlipChip requires accurate alignment of microfeatures on different plates; therefore, the dimensions of the microwells and density of partitions can be constrained. Here, we developed a droplet array SlipChip (da-SlipChip) that can form droplets of various sizes at high density in a single slipping step. This process does not require precise overlapping microfeatures on different plates; therefore, the design flexibility and partition density can be significantly increased. We quantified SARS-CoV-2 nucleic acids extracted from the COVID-19 pseudovirus by digital loop-mediated isothermal amplification (LAMP) on a da-SlipChip with 21 696 of 0.25 nL droplets, and the results were in good agreement with those of the commercial digital PCR method of Stilla. Furthermore, we demonstrated a random-access system with a single-throughput fluorescence imager and a stackable thermal control instrument with nine independent heating modules. This random-access system with the da-SlipChip can greatly improve the total throughput and flexibility for digital isothermal nucleic acid quantification and significantly reduce the total waiting time.
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Affiliation(s)
- Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
| | - Lei Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
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12
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Jiang M, Liao P, Sun Y, Shao X, Chen Z, Fei P, Wang J, Huang Y. Rotational scan digital LAMP for accurate quantitation of nucleic acids. LAB ON A CHIP 2021; 21:2265-2271. [PMID: 33908545 DOI: 10.1039/d1lc00114k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Digital quantitation of nucleic acids is precise and sensitive because of its molecular-level resolution. However, only several quantitation formats are common, especially pertaining to how one obtains digital signals from multiple droplets. Here we present rotational scan digital loop-mediated amplification, termed RS-dLAMP. Droplets generated by centrifugation undergo isothermal loop-mediated amplification (LAMP), and self-tile by gravitation into a tubular space between two coaxial cylinders, which are then rotated and scanned to acquire droplet fluorescence signals. RS-dLAMP is quantitatively comparable to commercial digital PCR, yet has higher throughput. Moreover, by sealing the sample throughout analysis, RS-dLAMP eliminates contamination, facilitating point-of-care diagnosis and other applications.
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Affiliation(s)
- Mengcheng Jiang
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Peiyu Liao
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Yue Sun
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xinyang Shao
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zitian Chen
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbin Wang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, China
| | - Yanyi Huang
- Materials Science and Engineering, College of Engineering, Peking University, Beijing, China. and Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China and College of Chemistry and Molecular Engineering, and, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China and Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
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13
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Xu G, Si H, Jing F, Sun P, Wu D. A Self-Priming Microfluidic Chip with Cushion Chambers for Easy Digital PCR. BIOSENSORS-BASEL 2021; 11:bios11050158. [PMID: 34069758 PMCID: PMC8155915 DOI: 10.3390/bios11050158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/17/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
A polydimethylsiloxane (PDMS)-based self-priming microfluidic chip with cushion chambers is presented in this study for robust and easy-operation digital polymerase chain reaction (dPCR). The chip has only one inlet and can partition samples autonomously through negative pressure, provided by a de-gassed PDMS layer with a multi-level vertical branching microchannel design. Meanwhile, cushion chambers make the chip capable of very robust use for sample partitioning. Finally, the proposed microfluidic chip showed excellent performance in the absolute quantification of a target gene by performing quantitative detection of a 10-fold serial dilution DNA template. Owing to its characteristics of easy operation, low cost, and high robustness, the proposed dPCR chip is expected to further promote the extensive application of digital PCR, especially in resource-limited settings.
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Affiliation(s)
- Gangwei Xu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
| | - Huaqing Si
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
| | - Fengxiang Jing
- Shanghai Turtle Technology Company Limited, Shanghai 200439, China;
| | - Peng Sun
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
| | - Dongping Wu
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China; (G.X.); (H.S.); (P.S.)
- Correspondence:
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14
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Honda S, Minagawa Y, Noji H, Tabata KV. Multidimensional Digital Bioassay Platform Based on an Air-Sealed Femtoliter Reactor Array Device. Anal Chem 2021; 93:5494-5502. [PMID: 33706506 DOI: 10.1021/acs.analchem.0c05360] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Single-molecule experiments have been helping us to get deeper inside biological phenomena by illuminating how individual molecules actually work. Digital bioassay, in which analyte molecules are individually confined in small compartments to be analyzed, is an emerging technology in single-molecule biology and applies to various biological entities (e.g., cells and virus particles). However, digital bioassay is not compatible with multiconditional and multiparametric assays, hindering in-depth understanding of analytes. This is because current digital bioassay lacks a repeatable solution-exchange system that keeps analytes inside compartments. To address this challenge, we developed a digital bioassay platform with easy solution exchanges, called multidimensional (MD) digital bioassay. We immobilized single analytes in arrayed femtoliter (10-15 L) reactors and sealed them with airflow. The solution in each reactor was stable and showed no cross-talk via solution leakage for more than 2 h, and over 30 rounds of perfect solution exchanges were successfully performed. With multiconditional assays based on our system, we could quantitatively determine inhibitor sensitivities of single influenza A virus particles and single alkaline phosphatase (ALP) molecules, which has never been achieved with conventional digital bioassays. Further, we demonstrated that ALPs from two origins can be precisely distinguished by a single-molecule multiparametric assay with our system, which was also difficult with conventional digital bioassays. Thus, MD digital bioassay is a versatile platform to gain in-depth insight into biological entities in unprecedented resolution.
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15
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Nanoporous hydrogel for direct digital nucleic acid amplification in untreated complex matrices for single bacteria counting. Biosens Bioelectron 2021; 184:113199. [PMID: 33887613 DOI: 10.1016/j.bios.2021.113199] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 12/28/2022]
Abstract
Direct quantification of pathogens in unprocessed complex samples remain challenging due to the severe inhibition of nucleic acid amplification. In this work, we report a nanoporous polyethylene glycol hydrogel with self-cleaning capacity for direct amplification of nucleic acid in complex matrices (human whole blood, animal blood, milky tea, humic acid, and surfactants) without any sample pretreatment or DNA extraction. During isothermal amplification inside the hydrogel, the inhibitors in the assay will be adsorbed and removed by the surrounding nanostructured polymers, and nucleic acid amplification was proceeding successfully, resulting in a series of bright dots for single bacteria counting. Thus, the loop-mediated isothermal amplifications (LAMP) performed inside hydrogel demonstrated a high level of resistance to inhibition in various complex matrices. The underlying anti-inhibition mechanism was also investigated. Digital quantification of Escherichia coli, Salmonella typhi and Listeria monocytogenes in whole blood were achieved within 20 min, with wide dynamic range, high specificity and low detection limit down to single bacterium. Visual counting via naked eye was also successfully established with the help of a conventional LED flashlight. We believe the developed hydrogel nanofluidic system has an enormous potential for on-site direct analysis of complex, crude, and unprocessed samples in clinical, food, agricultural, and environmental fields.
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16
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Ahrberg CD, Choi JW, Lee JM, Lee KG, Lee SJ, Manz A, Chung BG. Plasmonic heating-based portable digital PCR system. LAB ON A CHIP 2020; 20:3560-3568. [PMID: 32844858 DOI: 10.1039/d0lc00788a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A miniaturized polymerase chain reaction (PCR) system is not only important for medical applications in remote areas of developing countries, but also important for testing at ports of entry during global epidemics, such as the current outbreak of the coronavirus. Although there is a large number of PCR sensor systems available for this purpose, there is still a lack of portable digital PCR (dPCR) heating systems. Here, we first demonstrated a portable plasmonic heating-based dPCR system. The device has total dimensions of 9.7 × 5.6 × 4.1 cm and a total power consumption of 4.5 W, allowing for up to 25 dPCR experiments to be conducted on a single charge of a 20 000 mAh external battery. The dPCR system has a maximum heating rate of 10.7 °C s-1 and maximum cooling rate of 8 °C s-1. Target DNA concentrations in the range from 101 ± 1.4 copies per μL to 260 000 ± 20 000 copies per μL could be detected using a poly(dimethylsiloxane) (PDMS) microwell membrane with 22 080 well arrays (20 μm diameter). Furthermore, the heating system was demonstrated using a mass producible poly(methyl methacrylate) PMMA microwell array with 8100 microwell arrays (80 μm diameter). The PMMA microwell array could detect a concentration from 12 ± 0.7 copies per μL to 25 889 ± 737 copies per μL.
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17
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McCarthy Riley BF, Ward CL, Linz TH. Influence of microfabrication on digital PCR performance in bead-based microwell array assays. Anal Bioanal Chem 2020; 412:6917-6926. [PMID: 32772126 DOI: 10.1007/s00216-020-02822-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 11/25/2022]
Abstract
Digital PCR (dPCR) is a highly sensitive analytical technique used to quantify DNA targets. Detection sensitivity can be further enhanced by capturing target sequences onto beads for preconcentration and sample cleanup prior to analysis in microfluidic microwell arrays. However, robust digital analysis requires individual beads to be interrogated within individual wells. Fabricating microwells with dimensions ≤ 3 μm is challenging, and the high surface area-to-volume ratio of the wells leaves PCR susceptible to inhibition stemming from materials used during device processing. This report describes the development of a microfabrication procedure to create ultralow-volume wells (100 fL) for bead-based dPCR and characterize the effects of microprocessing materials on assay performance. Standard microfabrication protocols used for creating microelectronics resulted in devices with nanoscopic debris originating from photoresists used during processing. A model dPCR assay was developed to characterize the effects of this debris, which revealed variable PCR inhibition. Debris within microwells attenuated digital and analog assay signals to a greater extent than debris on the device surface. Spatial heterogeneity of debris across devices was quantified to characterize regional PCR inhibition and intra- and inter-device variability. Ultimately, a fabrication procedure was developed to create pristine microfluidic arrays using dual processes to remove positive resist and forgoing use of negative resist entirely, which enabled robust amplification with digital signals matching theoretical predictions. Results from this work catalog the unique performance artifacts from device microfabrication and provide a guide for future studies seeking to conduct robust, high-sensitivity bead-based dPCR assays. Graphical abstract.
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Affiliation(s)
| | - Cassandra L Ward
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA.
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18
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Cui X, Wu L, Wu Y, Zhang J, Zhao Q, Jing F, Yi L, Li G. Fast and robust sample self-digitization for digital PCR. Anal Chim Acta 2020; 1107:127-134. [PMID: 32200886 DOI: 10.1016/j.aca.2020.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/14/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023]
Abstract
We present a facile sample partitioning method to enable rapid and low-cost digital PCR (dPCR) assays. By subdividing a high percentage of the sample volume into a large number of equal volume compartments with a self-digitization (SD) chip, this method can achieve a low-waste and high-order sample discretization in a matter of minutes. The SD chip contains a set of parallel microfluidic channels used for sample delivery, and each channel is connected with two rows of cylindrical wells to hold the discretized sample. By utilizing a degassed PDMS sealing slab as a detachable vacuum pumping source, the SD chip automatically generate large arrays of small sample volumes without requirement of external pumping and valving components. Unlike most microfluidic chamber-based methods for sample discretization, our detachable SD chip allows for discretizing sample with air flushing, then peeling off the cover PDMS slab and sealing the digitized samples with oil layer. Due to obviation of time-consuming oil flushing, such microfluidic device can achieve much faster digitization of sample volumes. Furthermore, this digitization chip can partition more than 90% of a sample volume, which is important for the applications where the amount of material available is small. We also demonstrated the utility of the proposed SD chip by applying it to a dPCR assay.
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Affiliation(s)
- Xu Cui
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Lei Wu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Yin Wu
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Jinghong Zhang
- Shanghai Turtle Technology Company Limited, Shanghai, 200439, China
| | - Qiang Zhao
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Fengxiang Jing
- Shanghai Turtle Technology Company Limited, Shanghai, 200439, China.
| | - Lin Yi
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Gang Li
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China.
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19
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Zhou X, Ravichandran GC, Zhang P, Yang Y, Zeng Y. A microfluidic alternating-pull-push active digitization method for sample-loss-free digital PCR. LAB ON A CHIP 2019; 19:4104-4116. [PMID: 31720646 PMCID: PMC6894176 DOI: 10.1039/c9lc00932a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Digital polymerase chain reaction (dPCR) is a powerful tool for genetic analysis, providing superior sensitivity and accuracy. In many applications that demand minuscule reaction volumes, such as single cell analysis, efficient and reproducible sample handling and digitization is pivotal for accurate absolute quantification of targets, but remains a significant technical challenge. In this paper, we described a robust and flexible microfluidic alternating-pull-push active digitization (μAPPAD) strategy that confers close to 100% sample digitization efficiency for microwell-based dPCR. Our strategy employs pneumatic valve control to periodically manipulate air pressure inside the chip to greatly facilitate the vacuum-driven partition of solution into microwells, enabling efficient digitization of a small-volume solution with significantly reduced volume variability. The μAPPAD method was evaluated on both tandem-channel and parallel-channel chips, which achieved a digitization efficiency of 99.5 ± 0.3% and 94.6 ± 0.9% within 10.5 min and 2 min, respectively. To assess the analytical performance of the μAPPAD chip, we calibrated it for absolution dPCR quantitation of λDNA across a range of concentrations. The results obtained with our chip matched well with the theoretical curve computed from Poisson statistics. Compared to the existing methods for highly efficient sample digitization, not only does our technology greatly reduce the constraints on microwell geometries and channel design, but also benefits from the intrinsic amenability of the pneumatic valve technique with device integration and automation. Thus we envision that the μAPPAD technology will provide a scalable and widely adaptable platform to promote the development of advanced lab-on-a-chip systems integrating microscale sample processing with dPCR for a broad scope of applications, such as single cell analysis of tumor heterogeneity and genetic profiling of circulating exosomes directly in clinical samples.
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Affiliation(s)
- Xin Zhou
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | | | - Peng Zhang
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | - Yang Yang
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA. and University of Kansas Cancer Center, Kansas City, KS 66160, USA
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20
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Yu N, Liu Y, Wang S, Tang X, Ge P, Nan J, Zhang J, Yang B. Pressure-controlled microfluidic sub-picoliter ultramicro-volume syringes based on integrated micro-nanostructure arrays. LAB ON A CHIP 2019; 19:3368-3374. [PMID: 31549119 DOI: 10.1039/c9lc00730j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ultramicro-volume syringes were fabricated by integrating micro-nanostructure arrays in microchannels for quantitatively dispensing sub-picoliter volumes of liquids. Using this system, liquids were dispensed in volume increments as low as 0.5 pL with 96% accuracy. Specifically, the controllable synthesis of nanocrystals was achieved using a lab-on-chip platform that was integrated with the syringes.
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Affiliation(s)
- Nianzuo Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012, P. R. China.
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21
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Proximity ligation assays for precise quantification of femtomolar proteins in single cells using self-priming microfluidic dPCR chip. Anal Chim Acta 2019; 1076:118-124. [DOI: 10.1016/j.aca.2019.05.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/29/2019] [Accepted: 05/13/2019] [Indexed: 01/09/2023]
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22
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23
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Yu M, Chen X, Qu H, Ma L, Xu L, Lv W, Wang H, Ismagilov RF, Li M, Shen F. Multistep SlipChip for the Generation of Serial Dilution Nanoliter Arrays and Hepatitis B Viral Load Quantification by Digital Loop Mediated Isothermal Amplification. Anal Chem 2019; 91:8751-8755. [PMID: 31117407 DOI: 10.1021/acs.analchem.9b01270] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Serial dilution is a commonly used technique that generates a low-concentration working sample from a high-concentration stock solution and is used to set up screening conditions over a large dynamic range for biological study, optimization of reaction conditions, drug screening, etc. Creating an array of serial dilutions usually requires cumbersome manual pipetting steps or a robotic liquid handling system. Moreover, it is very challenging to set up an array of serial dilutions in nanoliter volumes in miniaturized assays. Here, a multistep SlipChip microfluidic device is presented for generating serial dilution nanoliter arrays in high throughput with a series of simple sliding motions. The dilution ratio can be precisely predetermined by the volumes of mother microwells and daughter microwells, and this paper demonstrates devices designed to have dilution ratios of 1:1, 1:2, and 1:4. Furthermore, an eight-step serial dilution SlipChip with a dilution ratio of 1:4 is applied for digital loop-mediated isothermal amplification (LAMP) across a large dynamic range and tested for hepatitis B viral load quantification with clinical samples. With 64 wells of each dilution and fewer than 600 wells in total, the serial dilution SlipChip can achieve a theoretical quantification dynamic range of 7 orders of magnitude.
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Affiliation(s)
- Mengchao Yu
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Xiaoying Chen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Haijun Qu
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Liang Ma
- Department of Chemistry and Institute for Biophysical Dynamics , The University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Lei Xu
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Weiyuan Lv
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
| | - Hua Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering , California Institute of Technology , 1200 East California Boulevard , Mail Code 210-41, Pasadena , California 91125 , United States.,Division of Biology & Biological Engineering , California Institute of Technology , 1200 East California Boulevard , Mail Code 210-41, Pasadena , California 91125 , United States
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China.,China State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100080 , China
| | - Feng Shen
- School of Biomedical Engineering , Shanghai Jiao Tong University , 1954 Hua Shan Road , Shanghai 200030 , China
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24
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Lin X, Huang X, Urmann K, Xie X, Hoffmann MR. Digital Loop-Mediated Isothermal Amplification on a Commercial Membrane. ACS Sens 2019; 4:242-249. [PMID: 30604619 PMCID: PMC6350201 DOI: 10.1021/acssensors.8b01419] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
In
this work, we report digital loop-mediated isothermal amplification
(LAMP) or reverse-transcription LAMP (RT-LAMP) on a commercial membrane,
without the need for complex chip fabrication or use of specialized
equipment. Due to the pore size distribution, the theoretical error
for digital LAMP on these membranes was analyzed, using a combination
of Random Distribution Model and Multivolume Theory. A facile peel-off
process was developed for effective droplet formation on the commercial
track-etched polycarbonate (PCTE) membrane. Each pore functions as
an individual nanoreactor for single DNA amplification. Absolute quantification
of bacteria genomic DNA was realized with a dynamic range from 11
to 1.1 × 105 copies/μL. One-step digital RT-LAMP
was also successfully performed on the membrane for the quantification
of MS2 virus in wastewater. With the introduction of new probes, the
positive pores can be easily distinguished from negative ones with
100 times difference in fluorescence intensities. Finally, the cost
of a disposable membrane is less than $0.10/piece, which, to the best
of our knowledge, is the most inexpensive way to perform digital LAMP.
The membrane system offers opportunities for point-of-care users or
common laboratories to perform digital quantification, single cell
analysis, or other bioassays in an inexpensive, flexible, and simplified
way.
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Affiliation(s)
- Xingyu Lin
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
| | - Xiao Huang
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
| | - Katharina Urmann
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
| | - Xing Xie
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Michael R. Hoffmann
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
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25
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Nie M, Zheng M, Li C, Shen F, Liu M, Luo H, Song X, Lan Y, Pan JZ, Du W. Assembled Step Emulsification Device for Multiplex Droplet Digital Polymerase Chain Reaction. Anal Chem 2019; 91:1779-1784. [DOI: 10.1021/acs.analchem.8b04313] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mengyue Nie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 10049, China
| | - Meng Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
| | - Caiming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 10049, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manhua Liu
- Department of Instrument Science and Engineering, The School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haibei Luo
- Pilot Gene Technologies, Hangzhou, 311203, China
| | - Xiaohui Song
- Pilot Gene Technologies, Hangzhou, 311203, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 10049, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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26
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Gou T, Hu J, Zhou S, Wu W, Fang W, Sun J, Hu Z, Shen H, Mu Y. A new method using machine learning for automated image analysis applied to chip-based digital assays. Analyst 2019; 144:3274-3281. [DOI: 10.1039/c9an00149b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An automated machine learning based method for image processes applied to digital assays.
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Affiliation(s)
- Tong Gou
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Jiumei Hu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Shufang Zhou
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Wenshuai Wu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Weibo Fang
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Jingjing Sun
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Zhenming Hu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Haotian Shen
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Ying Mu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
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27
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Ning Y, Cui X, Yang C, Jing F, Bian X, Yi L, Li G. A self-digitization chip integrated with hydration layer for low-cost and robust digital PCR. Anal Chim Acta 2018; 1055:65-73. [PMID: 30782371 DOI: 10.1016/j.aca.2018.12.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/15/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022]
Abstract
We present a self-discretization and zero-water-loss microfluidic digital PCR (dPCR) device to enable low-cost and robust quantitative nucleic acid assays. In this device, a thin void is integrated beneath the reaction chamber array. By utilizing the permeability of polydimethylsiloxane (PDMS) film, the integrated void serves a dual function: vacuum "accumulator" and hydration "reservoir". The combination of pre-stored pumping energy and water compensation for evaporation loss enables simple, robust and reliable single-DNA-molecule amplification and detection in 10,000 reactors of picoliter volume. Compared to the conventional degassing PDMS pumps, the vacuum accumulator exhibits superior performance due to more vacuum storage and shorter diffusion distance. We also evaluated the performance of the embedded hydration layer in suppressing evaporation loss at elevated temperatures, and verified that zero-water-loss could be achieved for all reaction chambers in our dPCR chip during thermal cycling. By performing quantitative detection of T790M DNA from 10 to 104 copies/μL, the proposed dPCR chip demonstrated high accuracy and excellent performance for the absolute quantification of the target gene with a dynamic range of 104. The simplicity and robustness of our dPCR chip make it well suited for low-cost molecular diagnostic assays under resource-limited settings.
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Affiliation(s)
- Yongfeng Ning
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Xu Cui
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Chao Yang
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China
| | - Fengxiang Jing
- Shanghai Turtle Technology Company Limited, Shanghai, 200439, China.
| | - Xiaojun Bian
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Lin Yi
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030, China
| | - Gang Li
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing, 400044, China.
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28
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Lin X, Huang X, Zhu Y, Urmann K, Xie X, Hoffmann MR. Asymmetric Membrane for Digital Detection of Single Bacteria in Milliliters of Complex Water Samples. ACS NANO 2018; 12:10281-10290. [PMID: 30211534 PMCID: PMC6202633 DOI: 10.1021/acsnano.8b05384] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/13/2018] [Indexed: 05/22/2023]
Abstract
In this work, we introduce an asymmetric membrane as a simple and robust nanofluidic platform for digital detection of single pathogenic bacteria directly in 10 mL of unprocessed environmental water samples. The asymmetric membrane, consisting of uniform micropores on one side and a high density of vertically aligned nanochannels on the other side, was prepared within 1 min by a facile method. The single membrane covers all the processing steps from sample concentration, purification, and partition to final digital loop-mediated isothermal amplification (LAMP). By simple filtration, bacteria were enriched and partitioned inside the micropores, while inhibitors typically found in the environmental samples ( i.e., proteins, heavy metals, and organics) were washed away through the nanochannels. Meanwhile, large particles, indigenous plankton, and positively charged pollutants in the samples were excluded by using a sacrificial membrane stacked on top. After initial filtration, modified LAMP reagents, including NaF and lysozyme, were loaded onto the membrane. Each pore in the asymmetric membrane functioned as an individual nanoreactor for selective, rapid, and efficient isothermal amplification of single bacteria, generating a bright fluorescence for direct counting. Even though high levels of inhibitors were present, absolute quantification of Escherichia coli and Salmonella directly in an unprocessed environmental sample (seawater and pond water) was achieved within 1 h, with sensitivity down to single cell and a dynamic range of 0.3-10000 cells/mL. The simple and low-cost analysis platform described herein has an enormous potential for the detection of pathogens, exosomes, stem cells, and viruses as well as single-cell heterogeneity analysis in environmental, food, and clinical research.
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Affiliation(s)
- Xingyu Lin
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xiao Huang
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Yanzhe Zhu
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Katharina Urmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xing Xie
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Michael R. Hoffmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
- E-mail:
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29
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Liao S, Tao Y, Du W, Wang Y. Interfacial Emulsification: An Emerging Monodisperse Droplet Generation Method for Microreactors and Bioanalysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11655-11666. [PMID: 29792711 DOI: 10.1021/acs.langmuir.8b01067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The generation of uniform droplets has been extensively investigated owing to its profound potentials both in scientific research and engineering applications. Although various methods have been put forward to expand this area, new innovations are still needed to improve the technical convenience and save instrumental cost. In this feature article, we highlight an interfacial emulsification technique that we developed in the past several years. This technique serves as a platform for preparing uniform droplets that are formed on the air-liquid interface of the continuous phase based on interfacial shearing. Three specific aspects of interfacial emulsification are reviewed, including its basic design and principle, the preparation of droplets with controllable size and adjustable components, and practical applications of the method in bioanalysis, microreactors, and particle synthesis. Compared to other droplet generation methods, several attractive advantages and perspectives for further development have been summarized.
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Affiliation(s)
- Shenglong Liao
- Department of Chemistry , Renmin University of China , Beijing 100872 , China
| | - Yi Tao
- State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China
- Savaid Medical School , University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China
- Savaid Medical School , University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Yapei Wang
- Department of Chemistry , Renmin University of China , Beijing 100872 , China
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30
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Yang H, Chen Z, Cao X, Li Z, Stavrakis S, Choo J, deMello AJ, Howes PD, He N. A sample-in-digital-answer-out system for rapid detection and quantitation of infectious pathogens in bodily fluids. Anal Bioanal Chem 2018; 410:7019-7030. [PMID: 30155705 DOI: 10.1007/s00216-018-1335-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/02/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022]
Abstract
A variety of automated sample-in-answer-out systems for in vitro molecular diagnostics have been presented and even commercialized. Although efficient in operation, they are incapable of quantifying targets, since quantitation based on analog analytical methods (via standard curve analysis) is complex, expensive, and challenging. To address this issue, herein, we describe an integrated sample-in-digital-answer-out (SIDAO) diagnostic system incorporating DNA extraction and digital recombinase polymerase amplification, which enables rapid and quantitative nucleic acid analysis from bodily fluids within a disposable cartridge. Inside the cartridge, reagents are pre-stored in sterilized tubes, with an automated pipetting module allowing facile liquid transfer. For digital analysis, we fabricate a simple, single-layer polydimethylsiloxane microfluidic device and develop a novel and simple sample compartmentalization strategy. Sample solution is partitioned into an array of 40,044 fL-volume microwells by sealing the microfluidic device through the application of mechanical pressure. The entire analysis is performed in a portable, fully automated instrument. We evaluate the quantitative capabilities of the system by analyzing Mycobacterium tuberculosis genomic DNA from both spiked saliva and serum samples, and demonstrate excellent analytical accuracy and specificity. This SIDAO system provides a promising diagnostic platform for quantitative nucleic acid testing at the point-of-care. Graphical abstract ᅟ.
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Affiliation(s)
- Haowen Yang
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Zhu Chen
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, Hunan, China.,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xiaobao Cao
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Zhiyang Li
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Sa-1-dong 1271, Ansan, 15588, South Korea
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland.
| | - Philip D Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Nongyue He
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, Hunan, China. .,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China.
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31
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Tsugane M, Suzuki H. Reverse Transcription Polymerase Chain Reaction in Giant Unilamellar Vesicles. Sci Rep 2018; 8:9214. [PMID: 29907779 PMCID: PMC6003926 DOI: 10.1038/s41598-018-27547-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/04/2018] [Indexed: 02/07/2023] Open
Abstract
We assessed the applicability of giant unilamellar vesicles (GUVs) for RNA detection using in vesicle reverse transcription polymerase chain reaction (RT-PCR). We prepared GUVs that encapsulated one-pot RT-PCR reaction mixture including template RNA, primers, and Taqman probe, using water-in-oil emulsion transfer method. After thermal cycling, we analysed the GUVs that exhibited intense fluorescence signals, which represented the cDNA amplification. The detailed analysis of flow cytometry data demonstrated that rRNA and mRNA in the total RNA can be amplified from 10–100 copies in the GUVs with 5–10 μm diameter, although the fraction of reactable GUV was approximately 60% at most. Moreover, we report that the target RNA, which was directly transferred into the GUV reactors via membrane fusion, can be amplified and detected using in vesicle RT-PCR. These results suggest that the GUVs can be used as biomimetic reactors capable of performing PCR and RT-PCR, which are important in analytical and diagnostic applications with additional functions.
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Affiliation(s)
- Mamiko Tsugane
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, Japan.,Japan Society for the Promotion of Science (JSPS), 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, Japan.
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32
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Zhang W, Li N, Koga D, Zhang Y, Zeng H, Nakajima H, Lin JM, Uchiyama K. Inkjet Printing Based Droplet Generation for Integrated Online Digital Polymerase Chain Reaction. Anal Chem 2018; 90:5329-5334. [DOI: 10.1021/acs.analchem.8b00463] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Weifei Zhang
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Nan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Daisuke Koga
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Yong Zhang
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Hulie Zeng
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Hizuru Nakajima
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Katsumi Uchiyama
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
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33
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Xu X, Yuan H, Song R, Yu M, Chung HY, Hou Y, Shang Y, Zhou H, Yao S. High aspect ratio induced spontaneous generation of monodisperse picolitre droplets for digital PCR. BIOMICROFLUIDICS 2018; 12:014103. [PMID: 29333205 PMCID: PMC5750054 DOI: 10.1063/1.5011240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/18/2017] [Indexed: 05/26/2023]
Abstract
Droplet microfluidics, which involves micrometer-sized emulsion droplets on a microfabricated platform, has been demonstrated as a unique system for many biological and chemical applications. Robust and scalable generation of monodisperse droplets at high throughput is of fundamental importance for droplet microfluidics. Classic designs for droplet generation employ shear fluid dynamics to induce the breakup of droplets in a two-phase flow and the droplet size is sensitive to flow rate fluctuations, often resulting in polydispersity. In this paper, we show spontaneous emulsification by a high aspect ratio (>3.5) rectangular nozzle structure. Due to the confinement and abrupt change of the structure, a Laplace pressure difference is generated between the dispersed and continuous phases, and causes the thread thinning and droplet pinch-off without the need to precisely control external flow conditions. A high-throughput droplet generator was developed by parallelization of a massive number of the basic structures. This device enabled facile and rapid partition of aqueous samples into millions of uniform picolitre droplets in oil. Using this device, on-chip droplet-based digital polymerase chain reaction (PCR) was performed for absolute quantification of rare genes with a wide dynamic range.
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Affiliation(s)
- Xiaonan Xu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Haojun Yuan
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai, China
| | - Ruyuan Song
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Miao Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ho Yin Chung
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Youmin Hou
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yuhe Shang
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbo Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai, China
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34
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Liao P, Huang Y. Digital PCR: Endless Frontier of 'Divide and Conquer'. MICROMACHINES 2017; 8:mi8080231. [PMID: 30400421 PMCID: PMC6189721 DOI: 10.3390/mi8080231] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 01/20/2023]
Abstract
Digital polymerase chain reaction (PCR) is becoming ever more recognized amid the overwhelming revolution in DNA quantification, genomics, genetics, and diagnostics led by technologies such as next generation sequencing and studies at the single-cell level. The demand to quantify the amount of DNA and RNA has been driven to the molecular level and digital PCR, with its unprecedented quantification capability, is sure to shine in the coming era. Two decades ago, it emerged as a concept; yet one decade ago, integration with microfluidics invigorated this field. Today, many methods have come to public knowledge and applications surrounding digital PCR is mounting. However, to reach wider accessibility and better practicality, efforts are needed to tackle the remaining problems. This perspective looks back at several inspiring and influential digital PCR approaches in the past and tries to provide a futuristic picture of the trends of digital PCR technologies to come.
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Affiliation(s)
- Peiyu Liao
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), College of Engineering, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), College of Engineering, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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35
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Sun M, Xie Y, Zhu J, Li J, Eijkel JCT. Improving the Resolution of 3D-Printed Molds for Microfluidics by Iterative Casting-Shrinkage Cycles. Anal Chem 2017; 89:2227-2231. [DOI: 10.1021/acs.analchem.6b05148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Miao Sun
- MOE
Key Laboratory of Space Applied Physics and Chemistry, School of Science, Northwestern Polytechnical University, Xi’an 710072, China
| | - Yanbo Xie
- MOE
Key Laboratory of Space Applied Physics and Chemistry, School of Science, Northwestern Polytechnical University, Xi’an 710072, China
| | - Jihong Zhu
- Engineering
Simulation and Aerospace Computing, School of Mechanical Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - Jun Li
- MOE
Key Laboratory of Space Applied Physics and Chemistry, School of Science, Northwestern Polytechnical University, Xi’an 710072, China
| | - Jan C. T. Eijkel
- BIOS−Lab
on a Chip Group, MESA+ Institute for Nanotechnology and MIRA Institute
for Biomedical Technology and Technical Medicine, University of Twente, 7522
NB Enschede, The Netherlands
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36
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Chen Z, Liao P, Zhang F, Jiang M, Zhu Y, Huang Y. Centrifugal micro-channel array droplet generation for highly parallel digital PCR. LAB ON A CHIP 2017; 17:235-240. [PMID: 28009866 DOI: 10.1039/c6lc01305h] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Stable water-in-oil emulsion is essential to digital PCR and many other bioanalytical reactions that employ droplets as microreactors. We developed a novel technology to produce monodisperse emulsion droplets with high efficiency and high throughput using a bench-top centrifuge. Upon centrifugal spinning, the continuous aqueous phase is dispersed into monodisperse droplet jets in air through a micro-channel array (MiCA) and then submerged into oil as a stable emulsion. We performed dPCR reactions with a high dynamic range through the MiCA approach, and demonstrated that this cost-effective method not only eliminates the usage of complex microfluidic devices and control systems, but also greatly suppresses the loss of materials and cross-contamination. MiCA-enabled highly parallel emulsion generation combines both easiness and robustness of picoliter droplet production, and breaks the technical challenges by using conventional lab equipment and supplies.
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Affiliation(s)
- Zitian Chen
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, and College of Engineering, Peking University, Beijing, China.
| | - Peiyu Liao
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, and College of Engineering, Peking University, Beijing, China.
| | - Fangli Zhang
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, and College of Engineering, Peking University, Beijing, China.
| | - Mengcheng Jiang
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, and College of Engineering, Peking University, Beijing, China.
| | - Yusen Zhu
- Integrated Science Program, Yuanpei College, Peking University, Beijing, China
| | - Yanyi Huang
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, and College of Engineering, Peking University, Beijing, China.
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37
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Abstract
The development of microfabricated devices that will provide high-throughput quantitative data and high resolution in a fast, repeatable and reproducible manner is essential for plant biology research.
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Affiliation(s)
- Meltem Elitaş
- Department of Mechatronics
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Meral Yüce
- Nanotechnology Research and Application Centre
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Hikmet Budak
- Department of Molecular Biology
- Genetics and Bioengineering
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
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38
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Hu Y, Xu P, Luo J, He H, Du W. Absolute Quantification of H5-Subtype Avian Influenza Viruses Using Droplet Digital Loop-Mediated Isothermal Amplification. Anal Chem 2016; 89:745-750. [PMID: 28105842 DOI: 10.1021/acs.analchem.6b03328] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human infection with avian influenza A H5N1 viruses can cause severe diseases with high mortality rate and continues to pose a significant threat to global public health. Rapid diagnosis is needed for identifying the types of influenza viruses for making timely treatment decisions. Here, we demonstrate absolute quantification of H5-subtype influenza viruses by digital loop-mediated isothermal amplification (dLAMP) on our recently developed cross-interface emulsification (XiE) method. Our results show that XiE-based dLAMP is highly specific and displays comparable sensitivity to real-time PCR (qPCR) and digital PCR (dPCR). Notably, dLAMP is more tolerant to inhibitory substances than PCR methods and demonstrated similar detection efficiency to qPCR for real H5N1 samples. Therefore, it can serve as a robust and precise alternative to qPCR or dPCR and is especially suitable for environmental and clinical samples with hard-to-remove contaminants. We believe that our dLAMP method offers great potential for rapid and accurate diagnosis of influenza and other infectious diseases.
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Affiliation(s)
- Yi Hu
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Peng Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Jing Luo
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Hongxuan He
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
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39
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Liu WW, Zhu Y, Feng YM, Fang J, Fang Q. Droplet-Based Multivolume Digital Polymerase Chain Reaction by a Surface-Assisted Multifactor Fluid Segmentation Approach. Anal Chem 2016; 89:822-829. [DOI: 10.1021/acs.analchem.6b03687] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wen-Wen Liu
- Institute of Microanalytical Systems, Department
of Chemistry and Innovation Center for Cell Signaling
Network, Zhejiang University, Hangzhou, 310058, China
| | - Ying Zhu
- Institute of Microanalytical Systems, Department
of Chemistry and Innovation Center for Cell Signaling
Network, Zhejiang University, Hangzhou, 310058, China
| | - Yi-Ming Feng
- Department
of Cell Biology, China Medical University, Shenyang, 110001, China
| | - Jin Fang
- Department
of Cell Biology, China Medical University, Shenyang, 110001, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department
of Chemistry and Innovation Center for Cell Signaling
Network, Zhejiang University, Hangzhou, 310058, China
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40
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Affiliation(s)
- Yi Zhang
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Japan Science and Technology Agency , Tokyo 102-0076, Japan
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41
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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Guardingo M, Busqué F, Ruiz-Molina D. Reactions in ultra-small droplets by tip-assisted chemistry. Chem Commun (Camb) 2016; 52:11617-26. [PMID: 27468750 DOI: 10.1039/c6cc03504c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The confinement of chemical reactions within small droplets has received much attention in the last few years. This approach has been proved successful for the in-depth study of naturally occurring chemical processes as well as for the synthesis of different sets of nanomaterials with control over their size, shape and properties. Different approaches such as the use of self-contained structures or microfluidic generated droplets have been followed over the years with success. However, novel approaches have emerged during the last years based on the deposition of femtolitre-sized droplets on surfaces using tip-assisted lithographic methods. In this feature article, we review the advances made towards the use of these ultra-small droplets patterned on surfaces as confined nano-reactors.
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Affiliation(s)
- M Guardingo
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra 08193, Barcelona, Spain.
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DING X, MU Y. Research and Application Progress of Digital Nucleic Acid Amplification Detection Techniques. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60918-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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The μSCAPE System: 3-Dimensional Profiling of Microfluidic Architectural Features Using a Flatbed Scanner. Sci Rep 2016; 6:22246. [PMID: 26924294 PMCID: PMC4770298 DOI: 10.1038/srep22246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 12/16/2022] Open
Abstract
We developed a microfluidic scanner-based profile exploration system, μSCAPE, capable of generating high resolution 3D profiles of microstructure architecture in a variety of transparent substrates. The profile is obtained by scanning the dye-filled microstructure followed by absorbance calculation and the reconstruction of the optical length at each point. The power of the method was demonstrated in (1) the inspection of the variation of the cross-section of laser-ablated PDMS channel; (2) the volume of PeT chamber; and (3) the population distribution of the volumes of the micro wells in HF-etched glass and laser-ablated PDMS. The reported methods features low equipment-cost, convenient operation and large field of view (FOV), and has revealed unreported quality parameters of the tested microstructures.
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Xu P, Zheng X, Tao Y, Du W. Cross-Interface Emulsification for Generating Size-Tunable Droplets. Anal Chem 2016; 88:3171-7. [DOI: 10.1021/acs.analchem.5b04510] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Xu
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu Zheng
- State
Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Tao
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbin Du
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Song Q, Gao Y, Zhu Q, Tian Q, Yu B, Song B, Xu Y, Yuan M, Ma C, Jin W, Zhang T, Mu Y, Jin Q. A nanoliter self-priming compartmentalization chip for point-of-care digital PCR analysis. Biomed Microdevices 2015; 17:64. [PMID: 26022215 DOI: 10.1007/s10544-015-9970-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A nanoliter self-priming compartmentalization (SPC) microfluidic chip suited for the digital polymerase chain reaction (dPCR) analysis in point-of-care testing (POCT) has been developed. This dPCR chip is fabricated of polydimethylsiloxane (PDMS). After the dPCR chip is evacuated, there will be a negative pressure environment in the chip because of the gas solubility of PDMS. The negative pressure environment can provide a self-priming power so that the sample solutions can be sucked into each reaction chamber sequentially. The whole sampling process requires no external power and is valve-free. Channels that contain water are designed around each sample panel to prevent the solvent (water) from evaporating during dPCR process. A glass coverslip is also used as a waterproof layer, which is more convenient and more efficient than other waterproof methods seen in literature. This dPCR chip allows three samples to be amplified at the same time. Each sample is distributed into 1040 reaction chambers, and each chamber is only 2.08 nL. Human β-actin DNA solutions of known concentrations are used as the templates for the dPCR analyses to verify the sensitivity and accuracy of the method. Template DNA solutions diluted to concentrations of 300, 100 and 10 copies/μL are tested and shown that this simple, portable and self-priming dPCR chip can be used at any clinic as a real POCT technique.
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Affiliation(s)
- Qi Song
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, People's Republic of China
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47
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An integrated microfluidic system for bovine DNA purification and digital PCR detection. Anal Biochem 2015; 491:55-7. [DOI: 10.1016/j.ab.2015.08.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/17/2022]
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48
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Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA. Scalable microfluidics for single-cell RNA printing and sequencing. Genome Biol 2015; 16:120. [PMID: 26047807 PMCID: PMC4487847 DOI: 10.1186/s13059-015-0684-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/27/2015] [Indexed: 11/21/2022] Open
Abstract
Many important biological questions demand single-cell transcriptomics on a large scale. Hence, new tools are urgently needed for efficient, inexpensive manipulation of RNA from individual cells. We report a simple platform for trapping single-cell lysates in sealed, picoliter microwells capable of printing RNA on glass or capturing RNA on beads. We then develop a scalable technology for genome-wide, single-cell RNA-Seq. Our device generates pooled libraries from hundreds of individual cells with consumable costs of $0.10–$0.20 per cell and includes five lanes for simultaneous experiments. We anticipate that this system will serve as a general platform for single-cell imaging and sequencing.
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Affiliation(s)
- Sayantan Bose
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Zhenmao Wan
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Ambrose Carr
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Abbas H Rizvi
- Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Gregory Vieira
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Dana Pe'er
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA. .,Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Peter A Sims
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA. .,Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA. .,Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY, 10032, USA.
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49
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Tian Q, Yu B, Mu Y, Xu Y, Ma C, Zhang T, Jin W, Jin Q. An integrated temporary negative pressure assisted microfluidic chip for DNA isolation and digital PCR detection. RSC Adv 2015. [DOI: 10.1039/c5ra18166f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An integrated DNA purification and digital PCR (dPCR) detection microfluidic chip was developed in this study.
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Affiliation(s)
- Qingchang Tian
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Baodong Yu
- China-Japan Union Hospital of Jilin University
- Changchun
- P. R. China
| | - Ying Mu
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Yanan Xu
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Congcong Ma
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Tao Zhang
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Wei Jin
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Qinhan Jin
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
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Microfluidic platform towards point-of-care diagnostics in infectious diseases. J Chromatogr A 2014; 1377:13-26. [PMID: 25544727 DOI: 10.1016/j.chroma.2014.12.041] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 01/09/2023]
Abstract
Rapid and timely diagnosis of infectious diseases is a critical determinant of clinical outcomes and general public health. For the detection of various pathogens, microfluidics-based platforms offer many advantages, including speed, cost, portability, high throughput, and automation. This review provides an overview of the recent advances in microfluidic technologies for point-of-care (POC) diagnostics for infectious diseases. The key aspects of such technologies for the development of a fully integrated POC platform are introduced, including sample preparation, on-chip nucleic acid analysis and immunoassay, and system integration/automation. The current challenges to practical implementation of this technology are discussed together with future perspectives.
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