1
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Jiao T, Sun P, Tian S, Tan Y, Wang C, He G, Shi L, Zhang Y, Li J, Gu Y. In Situ Colorimetric LAMP Based on One-Step Modified Filter Paper to Screen Human Papillomavirus (HPV)16/18 from Clinical Samples. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:16722-16730. [PMID: 39093056 PMCID: PMC11325640 DOI: 10.1021/acs.langmuir.4c00793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Cervical cancer is among the most common malignant tumors in women. The development of rapid screening techniques plays an important role in early screening for cancer treatment. We have developed an HPV screening method, which effectively combines the high-efficiency nucleic acid enrichment of chitosan-modified filter paper and the rapid visual detectability of colorimetric LAMP, along with the enhancement of the tolerance ability of the pH-sensitive LAMP reagent to acidic original samples, making the detection of HPV 16/18 easy to carry out and reliable, which is helpful for the epidemiological prevention and control strategies of HPV-induced cancer. This technique can simultaneously exhibit the "in situ amplification" capability of chitosan-modified filter paper and the nontemperature cycle dependence of visual LAMP detection. Therefore, DNA extraction and amplification can be performed efficiently and quickly within a single reaction where all DNA is concentrated in the QF paper disc. By embedding amino-modified filter paper into the plastic chip, a simple and reliable disposable chip was prepared for rapid HPV16 and HPV18 detection from clinical endometrial samples, and the results were 100% consistent with clinical diagnosis. More importantly, even after the sample was diluted 100-fold, HPV16/18-infected cells could be accurately identified, showing the advantages of the system in early cancer screening. Moreover, for endometrial samples containing plenty of cells, the filter paper could be used to enrich cells by filtration, preventing the acidic fluid from impacting pH-induced colorimetric LAMP detection and realizing direct amplification for HPV identification without nucleic acid extraction. This easy-to-operate system that can analyze a wide range of samples will be suitable for routine on-site HPV screening, dramatically extending the applications and utility for rapid, near-patient nucleic acid testing.
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Affiliation(s)
- Tingting Jiao
- Reproductive Medical Center, Department of Obstetrics and Gynecology, Seventh Medical Center of PLA General Hospital, Beijing 100700, China
| | - Peng Sun
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Shuang Tian
- Reproductive Medical Center, Department of Obstetrics and Gynecology, Seventh Medical Center of PLA General Hospital, Beijing 100700, China
| | - Yingjun Tan
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Chunyan Wang
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Guangjun He
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Liujia Shi
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Yang Zhang
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Jianhua Li
- Reproductive Medical Center, Department of Obstetrics and Gynecology, Seventh Medical Center of PLA General Hospital, Beijing 100700, China
| | - Yin Gu
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
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2
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Ge T, Hu W, Zhang Z, He X, Wang L, Han X, Dai Z. Open and closed microfluidics for biosensing. Mater Today Bio 2024; 26:101048. [PMID: 38633866 PMCID: PMC11022104 DOI: 10.1016/j.mtbio.2024.101048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Biosensing is vital for many areas like disease diagnosis, infectious disease prevention, and point-of-care monitoring. Microfluidics has been evidenced to be a powerful tool for biosensing via integrating biological detection processes into a palm-size chip. Based on the chip structure, microfluidics has two subdivision types: open microfluidics and closed microfluidics, whose operation methods would be diverse. In this review, we summarize fundamentals, liquid control methods, and applications of open and closed microfluidics separately, point out the bottlenecks, and propose potential directions of microfluidics-based biosensing.
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Affiliation(s)
- Tianxin Ge
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, PR China
| | - Wenxu Hu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, PR China
| | - Zilong Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, PR China
| | - Xuexue He
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, PR China
| | - Liqiu Wang
- Department of Mechanical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, PR China
| | - Xing Han
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, PR China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, PR China
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3
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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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4
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Panferov VG, Zherdev AV, Dzantiev BB. Post-Assay Chemical Enhancement for Highly Sensitive Lateral Flow Immunoassays: A Critical Review. BIOSENSORS 2023; 13:866. [PMID: 37754100 PMCID: PMC10526817 DOI: 10.3390/bios13090866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023]
Abstract
Lateral flow immunoassay (LFIA) has found a broad application for testing in point-of-care (POC) settings. LFIA is performed using test strips-fully integrated multimembrane assemblies containing all reagents for assay performance. Migration of liquid sample along the test strip initiates the formation of labeled immunocomplexes, which are detected visually or instrumentally. The tradeoff of LFIA's rapidity and user-friendliness is its relatively low sensitivity (high limit of detection), which restricts its applicability for detecting low-abundant targets. An increase in LFIA's sensitivity has attracted many efforts and is often considered one of the primary directions in developing immunochemical POC assays. Post-assay enhancements based on chemical reactions facilitate high sensitivity. In this critical review, we explain the performance of post-assay chemical enhancements, discuss their advantages, limitations, compared limit of detection (LOD) improvements, and required time for the enhancement procedures. We raise concerns about the performance of enhanced LFIA and discuss the bottlenecks in the existing experiments. Finally, we suggest the experimental workflow for step-by-step development and validation of enhanced LFIA. This review summarizes the state-of-art of LFIA with chemical enhancement, offers ways to overcome existing limitations, and discusses future outlooks for highly sensitive testing in POC conditions.
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Affiliation(s)
- Vasily G. Panferov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.G.P.); (A.V.Z.)
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.G.P.); (A.V.Z.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.G.P.); (A.V.Z.)
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5
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Panferov VG, Ivanov NA, Mazzulli T, Brinc D, Kulasingam V, Krylov SN. Electrophoresis-Assisted Multilayer Assembly of Nanoparticles for Sensitive Lateral Flow Immunoassay. Angew Chem Int Ed Engl 2023; 62:e202215548. [PMID: 36357330 DOI: 10.1002/anie.202215548] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Indexed: 11/12/2022]
Abstract
Lateral flow immunoassay (LFIA) is a rapid, simple, and inexpensive point-of-need method. A major limitation of LFIA is a high limit of detection (LOD), which impacts its diagnostic sensitivity. To overcome this limitation, we introduce a signal-enhancement procedure that is performed after completing LFIA and involves controllably moving biotin- and streptavidin-functionalized gold nanoparticles by electrophoresis. The nanoparticles link to immunocomplexes forming multilayer aggregates on the test strip, thus, enhancing the signal. Here, we demonstrate lowering the LOD of hepatitis B surface antigen from approximately 8 to 0.12 ng mL-1 , making it clinically acceptable. Testing 118 clinical samples for hepatitis B showed that signal enhancement increased the diagnostic sensitivity of LFIA from 73 % to 98 % while not affecting its 95 % specificity. Electrophoresis-driven enhancement of LFIA is universal (antigen-independent), takes two minutes, and can be performed by an untrained person.
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Affiliation(s)
- Vasily G Panferov
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,A.N. Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" Russian Academy of Sciences, 33 Leninsky Prospect, Moscow, 119071, Russia
| | - Nikita A Ivanov
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Tony Mazzulli
- Sinai Health, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Davor Brinc
- Toronto General Hospital: University Health Network, 200 Elizabeth St., Toronto, Ontario M5G 2C4, Canada
| | - Vathany Kulasingam
- Toronto General Hospital: University Health Network, 200 Elizabeth St., Toronto, Ontario M5G 2C4, Canada
| | - Sergey N Krylov
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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6
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Olanrewaju AO, Sullivan BP, Gim AH, Craig CA, Sevenler D, Bender AT, Drain PK, Posner JD. REverSe TRanscrIptase chain termination (RESTRICT) for selective measurement of nucleotide analogs used in HIV care and prevention. Bioeng Transl Med 2023; 8:e10369. [PMID: 36684094 PMCID: PMC9842053 DOI: 10.1002/btm2.10369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 01/25/2023] Open
Abstract
Sufficient drug concentrations are required for efficacy of antiretroviral drugs used in HIV care and prevention. Measurement of nucleotide analogs, included in most HIV medication regimens, enables monitoring of short- and long-term adherence and the risk of treatment failure. The REverSe TRanscrIptase Chain Termination (RESTRICT) assay rapidly infers the concentration of intracellular nucleotide analogs based on the inhibition of DNA synthesis by HIV reverse transcriptase enzyme. Here, we introduce a probabilistic model for RESTRICT and demonstrate selective measurement of multiple nucleotide analogs using DNA templates designed according to the chemical structure of each drug. We measure clinically relevant concentrations of tenofovir diphosphate, emtricitabine triphosphate, lamivudine triphosphate, and azidothymidine triphosphate with agreement between experiment and theory. RESTRICT represents a new class of activity-based assays for therapeutic drug monitoring in HIV care and could be extended to other diseases treated with nucleotide analogs.
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Affiliation(s)
- Ayokunle O. Olanrewaju
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Benjamin P. Sullivan
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Alicia H. Gim
- Department of Chemical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Cosette A. Craig
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Derin Sevenler
- Center for Engineering in Medicine and SurgeryMassachusetts General HospitalBostonMassachusettsUSA
| | - Andrew T. Bender
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Paul K. Drain
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
- Department of Global HealthUniversity of WashingtonSeattleWashingtonUSA
- Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Jonathan D. Posner
- Department of Mechanical EngineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of Chemical EngineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of Family MedicineUniversity of WashingtonSeattleWashingtonUSA
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7
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Chia CT, Bender AT, Lillis L, Sullivan BP, Martin CD, Burke W, Landis C, Boyle DS, Posner JD. Rapid detection of hepatitis C virus using recombinase polymerase amplification. PLoS One 2022; 17:e0276582. [PMID: 36282844 PMCID: PMC9595512 DOI: 10.1371/journal.pone.0276582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Over 71 million people are infected with hepatitis C virus (HCV) worldwide, and approximately 400,000 global deaths result from complications of untreated chronic HCV. Pan-genomic direct-acting antivirals (DAAs) have recently become widely available and feature high cure rates in less than 12 weeks of treatment. The rollout of DAAs is reliant on diagnostic tests for HCV RNA to identify eligible patients with viremic HCV infections. Current PCR-based HCV RNA assays are restricted to well-resourced central laboratories, and there remains a prevailing clinical need for expanded access to decentralized HCV RNA testing to provide rapid chronic HCV diagnosis and linkage to DAAs in outpatient clinics. This paper reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using reverse transcription recombinase polymerase amplification (RT-RPA). The assay detects all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1, the most prevalent in the United States and worldwide. The clinical sensitivity and specificity of the RT-RPA assay were both 100% when evaluated using 78 diverse clinical serum specimens. The accuracy, short runtime, and low heating demands of RT-RPA may enable implementation in a point-of-care HCV test to expand global access to effective treatment via rapid chronic HCV diagnosis.
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Affiliation(s)
- Catherine T. Chia
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Andrew T. Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | | | - Benjamin P. Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Coleman D. Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Wynn Burke
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Charles Landis
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
| | | | - Jonathan D. Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- Family Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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8
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Valloly P, Roy R. Nucleic Acid Quantification with Amplicon Yield in Recombinase Polymerase Amplification. Anal Chem 2022; 94:13897-13905. [PMID: 36170603 DOI: 10.1021/acs.analchem.2c02810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amplification-based quantitative polymerase chain reaction (qPCR) provides accurate and sensitive nucleic acid quantification. However, the requirement of temperature cycling and real-time monitoring limits its translation to many settings. Quantitative isothermal amplification methods alleviate the need for thermal cyclers; however, they still require continuous monitoring of the nucleic acid amplification on sophisticated readers. Here, we adapted an isothermal recombinase polymerase amplification (RPA) reaction to develop a semiquantitative method that relies on the final amplicon yield to estimate the initial target nucleic acid copy number. To achieve this, we developed a phenomenological model that captures the essential RPA dynamics. We identified reaction conditions that constrained the reaction yield corresponding to the starting DNA template concentration. We validated these predictions experimentally and showed that the amplicon yields at the end of the RPA reaction correlated well with the starting DNA concentration while reducing nonspecific amplification robustly. We demonstrate this approach, termed quantitative endpoint RPA (qeRPA), to detect DNA over five log orders with a detection limit of 100 molecules. Using a linear regression model of the normalized endpoint intensity (NEI) standard curve, we estimate the viral load from the serum of dengue virus-infected patients with comparable performance to qPCR. Unlike the conventional isothermal quantitative methods, qeRPA can be employed for robust and sensitive nucleic acid estimation at close to room temperature without real-time monitoring and can be beneficial for field deployment in resource-limited settings.
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Affiliation(s)
- Priyanka Valloly
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India 560012
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India 560012.,Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India 560012
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9
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Chavez‐Pineda OG, Rodriguez‐Moncayo R, Cedillo‐Alcantar DF, Guevara‐Pantoja PE, Amador‐Hernandez JU, Garcia‐Cordero JL. Microfluidic systems for the analysis of blood‐derived molecular biomarkers. Electrophoresis 2022; 43:1667-1700. [DOI: 10.1002/elps.202200067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Oriana G. Chavez‐Pineda
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Roberto Rodriguez‐Moncayo
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Diana F. Cedillo‐Alcantar
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Pablo E. Guevara‐Pantoja
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Josue U. Amador‐Hernandez
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Jose L. Garcia‐Cordero
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
- Roche Institute for Translational Bioengineering (ITB) Roche Pharma Research and Early Development, Roche Innovation Center Basel Basel Switzerland
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10
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Abstract
Isotachophoresis (ITP) is a versatile electrophoretic technique that can be used for sample preconcentration, separation, purification, and mixing, and to control and accelerate chemical reactions. Although the basic technique is nearly a century old and widely used, there is a persistent need for an easily approachable, succinct, and rigorous review of ITP theory and analysis. This is important because the interest and adoption of the technique has grown over the last two decades, especially with its implementation in microfluidics and integration with on-chip chemical and biochemical assays. We here provide a review of ITP theory starting from physicochemical first-principles, including conservation of species, conservation of current, approximation of charge neutrality, pH equilibrium of weak electrolytes, and so-called regulating functions that govern transport dynamics, with a strong emphasis on steady and unsteady transport. We combine these generally applicable (to all types of ITP) theoretical discussions with applications of ITP in the field of microfluidic systems, particularly on-chip biochemical analyses. Our discussion includes principles that govern the ITP focusing of weak and strong electrolytes; ITP dynamics in peak and plateau modes; a review of simulation tools, experimental tools, and detection methods; applications of ITP for on-chip separations and trace analyte manipulation; and design considerations and challenges for microfluidic ITP systems. We conclude with remarks on possible future research directions. The intent of this review is to help make ITP analysis and design principles more accessible to the scientific and engineering communities and to provide a rigorous basis for the increased adoption of ITP in microfluidics.
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Affiliation(s)
- Ashwin Ramachandran
- Department of Aeronautics and Astronautics, Stanford University, Stanford, California 94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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11
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Sullivan BP, Chou YS, Bender AT, Martin CD, Kaputa ZG, March H, Song M, Posner JD. Quantitative isothermal amplification on paper membranes using amplification nucleation site analysis. LAB ON A CHIP 2022; 22:2352-2363. [PMID: 35548880 PMCID: PMC9202034 DOI: 10.1039/d2lc00007e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and viral RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Yu-Shan Chou
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Coleman D Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Zoe G Kaputa
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Hugh March
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Minyung Song
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
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12
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Hang Y, Boryczka J, Wu N. Visible-light and near-infrared fluorescence and surface-enhanced Raman scattering point-of-care sensing and bio-imaging: a review. Chem Soc Rev 2022; 51:329-375. [PMID: 34897302 PMCID: PMC9135580 DOI: 10.1039/c9cs00621d] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This review article deals with the concepts, principles and applications of visible-light and near-infrared (NIR) fluorescence and surface-enhanced Raman scattering (SERS) in in vitro point-of-care testing (POCT) and in vivo bio-imaging. It has discussed how to utilize the biological transparency windows to improve the penetration depth and signal-to-noise ratio, and how to use surface plasmon resonance (SPR) to amplify fluorescence and SERS signals. This article has highlighted some plasmonic fluorescence and SERS probes. It has also reviewed the design strategies of fluorescent and SERS sensors in the detection of metal ions, small molecules, proteins and nucleic acids. Particularly, it has provided perspectives on the integration of fluorescent and SERS sensors into microfluidic chips as lab-on-chips to realize point-of-care testing. It has also discussed the design of active microfluidic devices and non-paper- or paper-based lateral flow assays for in vitro diagnostics. In addition, this article has discussed the strategies to design in vivo NIR fluorescence and SERS bio-imaging platforms for monitoring physiological processes and disease progression in live cells and tissues. Moreover, it has highlighted the applications of POCT and bio-imaging in testing toxins, heavy metals, illicit drugs, cancers, traumatic brain injuries, and infectious diseases such as COVID-19, influenza, HIV and sepsis.
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Affiliation(s)
- Yingjie Hang
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003-9303, USA.
| | - Jennifer Boryczka
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003-9303, USA.
| | - Nianqiang Wu
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003-9303, USA.
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13
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Recombinase polymerase amplification integrated with microfluidics for nucleic acid testing at point of care. Talanta 2022; 240:123209. [PMID: 35026642 DOI: 10.1016/j.talanta.2022.123209] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid testing (NAT) implemented on a portable, miniaturized, and integrated device with rapid and sensitive results readout is highly demanded for pathogen detection or genetic screening at resource-limited settings, especially after the outbreak of coronavirus disease 2019 (COVID-19). The integration of recombinase polymerase amplification (RPA) with emerging microfluidics, classified by paper-based microfluidics and chip-based microfluidics, shows great potential to perform laboratory independent NAT assays at point of care with minimal labor, time and energy consumption. This review summarizes the state-of-the-art of RPA integrated with paper-based microfluidics and chip-based microfluidics, and discusses their pros and cons. Finally, existing challenges and possible ways for optimization of microfluidics-based RPA are proposed.
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14
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Yost J, Gagnon Z. Faradaic-free electrokinetic nucleic acid amplification (E-NAAMP) using localized on-chip high frequency Joule heating. BIOMICROFLUIDICS 2022; 16:014101. [PMID: 35111277 PMCID: PMC8791667 DOI: 10.1063/5.0072198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
We present a novel Faradaic reaction-free nucleic acid amplification (NAA) method for use with microscale liquid samples. Unlike previous Joule heating methods where the electrodes produce electrolysis gaseous by-products and require both the electrodes be isolated from a sample and the venting of produced electrolysis gas, our electrokinetic Nucleic Acid Amplification (E-NAAMP) method alleviates these issues using a radio frequency (RF) alternating current electric field. In this approach, a pair of microscale thin film gold electrodes are placed directly in contact with a nucleic acid reaction mixture. A high frequency (10-40 MHz) RF potential is then applied across the electrode pair to induce a local Ohmic current within the sample and drive the sample temperature to increase by Joule heating. The temperature increase is sustainable in that it can be generated for several hours of constant use without generating any pH change to the buffer or any microscopically observable gaseous electrolysis by-products. Using this RF Joule heating approach, we demonstrate successful direct thermal amplification using two popular NAA biochemical reactions: loop-mediated isothermal amplification and polymerase chain reaction. Our results demonstrate that a simple microscale electrode structure can be used for thermal regulation for NAA reactions without observable electrolytic reactions, minimal enzyme activity loss and sustained (>50 h use per device) continuous operations without electrode delamination. As such, E-NAAMP offers substantial miniaturization of the heating elements for use in microfluidic or miniaturized NAA reaction systems.
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Affiliation(s)
- Jarad Yost
- Department of Chemical Engineering, Texas A&M University, 201 Jack E. Brown Building, College Station, Texas 77843, USA
| | - Zachary Gagnon
- Department of Chemical Engineering, Texas A&M University, 201 Jack E. Brown Building, College Station, Texas 77843, USA
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15
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Alahmad W, Sahragard A, Varanusupakul P. Online and offline preconcentration techniques on paper-based analytical devices for ultrasensitive chemical and biochemical analysis: A review. Biosens Bioelectron 2021; 194:113574. [PMID: 34474275 DOI: 10.1016/j.bios.2021.113574] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/24/2022]
Abstract
Microfluidic paper-based analytical devices (μPADs) have attracted much attention over the past decade. They embody many advantages, such as abundance, portability, cost-effectiveness, and ease of fabrication, making them superior for clinical diagnostics, environmental monitoring, and food safety assurance. Despite these advantages, μPADs lack the high sensitivity to detect many analytes at trace levels than other commercial analytical instruments such as mass spectrometry. Therefore, a preconcentration step is required to enhance their sensitivity. This review focuses on the techniques used to separate and preconcentrate the analytes onto the μPADs, such as ion concentration polarization, isotachophoresis, and field amplification sample stacking. Other separations and preconcentration techniques, including liquid-solid and liquid-liquid extractions coupled with μPADs, are also reviewed and discussed. In addition, the fabrication methods, advantages, disadvantages, and the performance evaluation of the μPADs concerning their precision and accuracy were highlighted and critically assessed. Finally, the challenges and future perspectives have been discussed.
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Affiliation(s)
- Waleed Alahmad
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Ali Sahragard
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pakorn Varanusupakul
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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16
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Chen H, Sun C, Wang Y, Gao X, You J, Yu W, Sun N, Yang Y, Li X. Rapid Detection of SARS-CoV-2 Using Duplex Reverse Transcription-Multienzyme Isothermal Rapid Amplification in a Point-of-Care Testing. Front Cell Infect Microbiol 2021; 11:678703. [PMID: 34746020 PMCID: PMC8569318 DOI: 10.3389/fcimb.2021.678703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
In December 2019, a severe acute respiratory syndrome caused by SARS-CoV-2 spread rapidly worldwide. Portable nucleic acid tests of SARS-CoV-2 are critically important for diagnostics. In this study, we used an isothermal amplification method-Multienzyme Isothermal Rapid Amplification (MIRA)-for rapid detection of SARS-CoV-2. We designed the primers and probes in ORF1ab and N gene of SARS-CoV-2. The amplicons could be monitored by lateral flow dipsticks (LFDs). The reaction temperature, time, concentrations of primers and probes, and working volume were optimized. Four commercial swab collection buffers were used to test the amplification efficacy of our assay without RNA extraction. Our assay was able to amplify duplex targets of SARS-CoV-2 in one single reaction using one-step RT-MIRA. The assay worked well in a low volume of 10 μl at 38°C for 20 min. Using three collection buffers without guanidinium, our assay was able to amplify efficaciously without RNA extraction. The 95% limit of detection (LoD) of the RT-MIRA assay was 49.5 (95% CI, 46.8-52.7) copies/ml for ORF1ab gene and 48.8 (95% CI, 46.5-52.6) copies/ml for N gene. There is no cross-reaction with other human respiratory pathogens, such as SARS-CoV, MERS-CoV, influenza A virus, influenza B virus, human adenovirus, respiratory syncytial virus, human parainfluenza virus, and coronavirus 229E in our assay. The precision evaluation revealed that the C50-20% to C50+20% range bounds the C5-C95 interval. This assay also showed high anti-interference ability. The extraction-free RT-MIRA and qPCR detection results of 243 nucleic acid specimens from suspected patients or national references showed a 100.0% (95% confidence interval, 94.2%-100.0%) positive predictive value and a 100.0% (95% confidence interval, 92.7%-100.0%) negative predictive value. Compared with qPCR, the kappa value of the two assays was 1.00 (P < 0.0001). In conclusion, we provide a portable and visualized method for detection of SARS-CoV-2 without RNA extraction, allowing its application in SARS-CoV-2 on-site detection.
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Affiliation(s)
- Hui Chen
- Department of Medicine, JiangSu University, Zhenjiang, China.,Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Chang Sun
- Department of Orthopaedics, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yang Wang
- Department of Orthopaedics, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Xiaojiao Gao
- Department of Clinical Laboratory, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Jinwei You
- Department of Laboratory Animal, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Wanwan Yu
- Department of Emergency, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Ning Sun
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yang Yang
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Xiaojun Li
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China.,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, China
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17
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Bender AT, Sullivan BP, Zhang JY, Juergens DC, Lillis L, Boyle DS, Posner JD. HIV detection from human serum with paper-based isotachophoretic RNA extraction and reverse transcription recombinase polymerase amplification. Analyst 2021; 146:2851-2861. [PMID: 33949378 PMCID: PMC9151496 DOI: 10.1039/d0an02483j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The number of people living with HIV continues to increase with the current total near 38 million, of which about 26 million are receiving antiretroviral therapy (ART). These treatment regimens are highly effective when properly managed, requiring routine viral load monitoring to assess successful viral suppression. Efforts to expand access by decentralizing HIV nucleic acid testing in low- and middle-income countries (LMICs) has been hampered by the cost and complexity of current tests. Sample preparation of blood samples has traditionally relied on cumbersome RNA extraction methods, and it continues to be a key bottleneck for developing low-cost POC nucleic acid tests. We present a microfluidic paper-based analytical device (μPAD) for extracting RNA and detecting HIV in serum, leveraging low-cost materials, simple buffers, and an electric field. We detect HIV virions and MS2 bacteriophage internal control in human serum using a novel lysis and RNase inactivation method, paper-based isotachophoresis (ITP) for RNA extraction, and duplexed reverse transcription recombinase polymerase amplification (RT-RPA) for nucleic acid amplification. We design a specialized ITP system to extract and concentrate RNA, while excluding harsh reagents used for lysis and RNase inactivation. We found the ITP μPAD can extract and purify 5000 HIV RNA copies per mL of serum. We then demonstrate detection of HIV virions and MS2 bacteriophage in human serum within 45-minutes.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, USA.
| | - David C Juergens
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | | | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, USA. and Department of Chemical Engineering, University of Washington, Seattle, USA and Family Medicine, School of Medicine, University of Washington, Seattle, USA
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18
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Zhang JY, Bender AT, Boyle DS, Drain PK, Posner JD. Current state of commercial point-of-care nucleic acid tests for infectious diseases. Analyst 2021; 146:2449-2462. [PMID: 33899053 PMCID: PMC8139840 DOI: 10.1039/d0an01988g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic has put the spotlight on the urgent need for integrated nucleic acid tests (NATs) for infectious diseases, especially those that can be used near patient ("point-of-care", POC), with rapid results and low cost, but without sacrificing sensitivity or specificity of gold standard PCR tests. In the US, the Clinical Laboratory Improvement Amendments Certificate of Waiver (CLIA-waiver) is mandated by the Food and Drug Administration (FDA) and designated to any laboratory testing with high simplicity and low risk for error, suitable for application in the POC. Since the first issuance of CLIA-waiver to Abbot's ID NOW Influenza A&B in 2015, many more NAT systems have been developed, received the CLIA-waiver in the US or World Health Organization (WHO)'s pre-qualification, and deployed to the front line of infectious disease detection. This review highlights the regulatory process for FDA and WHO in evaluating these NATs and the technology innovation of existing CLIA-waived systems. Understanding the technical advancement and challenges, unmet needs, and the trends of commercialization facilitated through the regulatory processes will help pave the foundation for future development and technology transfer from research to the market place.
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Affiliation(s)
- Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, USA.
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19
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Wang C, Liu M, Wang Z, Li S, Deng Y, He N. Point-of-care diagnostics for infectious diseases: From methods to devices. NANO TODAY 2021; 37:101092. [PMID: 33584847 PMCID: PMC7864790 DOI: 10.1016/j.nantod.2021.101092] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 05/04/2023]
Abstract
The current widespread of COVID-19 all over the world, which is caused by SARS-CoV-2 virus, has again emphasized the importance of development of point-of-care (POC) diagnostics for timely prevention and control of the pandemic. Compared with labor- and time-consuming traditional diagnostic methods, POC diagnostics exhibit several advantages such as faster diagnostic speed, better sensitivity and specificity, lower cost, higher efficiency and ability of on-site detection. To achieve POC diagnostics, developing POC detection methods and correlated POC devices is the key and should be given top priority. The fast development of microfluidics, micro electro-mechanical systems (MEMS) technology, nanotechnology and materials science, have benefited the production of a series of portable, miniaturized, low cost and highly integrated POC devices for POC diagnostics of various infectious diseases. In this review, various POC detection methods for the diagnosis of infectious diseases, including electrochemical biosensors, fluorescence biosensors, surface-enhanced Raman scattering (SERS)-based biosensors, colorimetric biosensors, chemiluminiscence biosensors, surface plasmon resonance (SPR)-based biosensors, and magnetic biosensors, were first summarized. Then, recent progresses in the development of POC devices including lab-on-a-chip (LOC) devices, lab-on-a-disc (LOAD) devices, microfluidic paper-based analytical devices (μPADs), lateral flow devices, miniaturized PCR devices, and isothermal nucleic acid amplification (INAA) devices, were systematically discussed. Finally, the challenges and future perspectives for the design and development of POC detection methods and correlated devices were presented. The ultimate goal of this review is to provide new insights and directions for the future development of POC diagnostics for the management of infectious diseases and contribute to the prevention and control of infectious pandemics like COVID-19.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, PR China
| | - Mei Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, PR China
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20
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Brunauer A, Verboket RD, Kainz DM, von Stetten F, Früh SM. Rapid Detection of Pathogens in Wound Exudate via Nucleic Acid Lateral Flow Immunoassay. BIOSENSORS-BASEL 2021; 11:bios11030074. [PMID: 33800856 PMCID: PMC8035659 DOI: 10.3390/bios11030074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
The rapid detection of pathogens in infected wounds can significantly improve the clinical outcome. Wound exudate, which can be collected in a non-invasive way, offers an attractive sample material for the detection of pathogens at the point-of-care (POC). Here, we report the development of a nucleic acid lateral flow immunoassay for direct detection of isothermally amplified DNA combined with fast sample preparation. The streamlined protocol was evaluated using human wound exudate spiked with the opportunistic pathogen Pseudomonas aeruginosa that cause severe health issues upon wound colonization. A detection limit of 2.1 × 105 CFU per mL of wound fluid was achieved, and no cross-reaction with other pathogens was observed. Furthermore, we integrated an internal amplification control that excludes false negative results and, in combination with the flow control, ensures the validity of the test result. The paper-based approach with only three simple hands-on steps has a turn-around time of less than 30 min and covers the complete analytical process chain from sample to answer. This newly developed workflow for wound fluid diagnostics has tremendous potential for reliable pathogen POC testing and subsequent target-oriented therapy.
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Affiliation(s)
- Anna Brunauer
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - René D Verboket
- Department of Trauma-, Hand- and Reconstructive Surgery, University Hospital Frankfurt, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Daniel M Kainz
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Susanna M Früh
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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21
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Li Z, Bai Y, You M, Hu J, Yao C, Cao L, Xu F. Fully integrated microfluidic devices for qualitative, quantitative and digital nucleic acids testing at point of care. Biosens Bioelectron 2020; 177:112952. [PMID: 33453463 PMCID: PMC7774487 DOI: 10.1016/j.bios.2020.112952] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
Benefiting from emerging miniaturized and equipment-free nucleic acid testing (NAT) technologies, fully integrated NAT devices at point of care (POC) with the capability of "sample-in-answer-out" are proceeding at a break-neck speed to eliminate complex operations and reduce the risk of contamination. Like the development of polymerase chain reaction (PCR) technology (the standard technique for NAT), the detection signal of fully integrated NAT devices has evolved from qualitative to quantitative and recently to digital readout, aiming at expanding their extensive applications through gradually improving detection sensitivity and accuracy. This review firstly introduces the existing commercial products, and then illustrates recent fully integrated microfluidic devices for NAT at POC from the aspect of detection signals (i.e., qualitative, quantitative and digital). Importantly, the key issues of existing commercial products and the main challenges between scientific research and product development are discussed. On this basis, we envision that the MARCHED (miniaturized, automatic, reagent-preloaded, commercializable, high-throughput, environment-independent and disposable) NAT devices are expected to be realized in the near future.
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Affiliation(s)
- Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Yuemeng Bai
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Jie Hu
- Suzhou DiYinAn Biotechnology Co., Ltd, Suzhou, 215010, PR China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
| | - Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
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22
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Sullivan BP, Bender AT, Ngyuen DN, Zhang JY, Posner JD. Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1163:122494. [PMID: 33401049 DOI: 10.1016/j.jchromb.2020.122494] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023]
Abstract
Nucleic acid amplification tests (NAATs) are a crucial diagnostic and monitoring tool for infectious diseases. A key procedural step for NAATs is sample preparation: separating and purifying target nucleic acids from crude biological samples prior to nucleic acid amplification and detection. Traditionally, sample preparation has been performed with liquid- or solid-phase extraction, both of which require multiple trained user steps and significant laboratory equipment. The challenges associated with sample preparation have limited the dissemination of NAAT point-of-care diagnostics in low resource environments, including low- and middle-income countries. We report on a paper-based device for purification of nucleic acids from whole blood using isotachophoresis (ITP) for point-of-care NAATs. We show successful extraction and purification of target nucleic acids from large volumes (33 µL) of whole human blood samples with no moving parts and few user steps. Our device utilizes paper-based buffer reservoirs to fully contain the liquid ITP buffers and does not require complex filling procedures, instead relying on the natural wicking of integrated paper membranes. We perform on-device blood fractionation via filtration to remove leukocytes and erythrocytes from our sample, followed by integrated on-paper proteolytic digestion of endogenous plasma proteins to allow for successful isotachophoretic extraction. Paper-based isotachophoresis purifies and concentrates target nucleic acids that are added directly to recombinase polymerase amplification (RPA) reactions. We show consistent amplification of input copy concentrations of as low as 3 × 103 copies nucleic acid per mL input blood with extraction and purification taking only 30 min. By employing a paper architecture, we are able to incorporate these processes in a single, robust, low-cost design, enabling the direct processing of large volumes of blood, with the only intermediate user steps being the removal and addition of tape. Our device represents a step towards a simple, fully integrated sample preparation system for nucleic acid amplification tests at the point-of-care.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Duy N Ngyuen
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jane Yuqian Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA; Department of Chemical Engineering, University of Washington, Seattle, WA, USA; Department of Family Medicine, University of Washington, Seattle, WA, USA.
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23
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, 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
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, 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
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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24
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Paul R, Ostermann E, Wei Q. Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases. Biosens Bioelectron 2020; 169:112592. [PMID: 32942143 PMCID: PMC7476893 DOI: 10.1016/j.bios.2020.112592] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022]
Abstract
Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.
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Affiliation(s)
- Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emily Ostermann
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA; Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, 27695, USA.
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25
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Spitzberg JD, van Kooten XF, Bercovici M, Meller A. Microfluidic device for coupling isotachophoretic sample focusing with nanopore single-molecule sensing. NANOSCALE 2020; 12:17805-17811. [PMID: 32820758 DOI: 10.1039/d0nr05000h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Solid-state nanopores (NPs) are label-free single-molecule sensors, capable of performing highly sensitive assays from a small number of biomolecule translocation events. However, single-molecule sensing is challenging at extremely low analyte concentrations due to the limited flux of analytes to the sensing volume. This leads to a low event rate and increases the overall assay time. In this work, we present a method to enhance the event rate at low analyte concentrations by using isotachophoresis (ITP) to focus and deliver analytes to a nanopore sensor. Central to this method is a device capable of performing ITP focusing directly on a solid-state NP chip, while preventing the focusing electric field from damaging the nanopore membrane. We discuss considerations and trade-offs related to the design of the focusing channel, the ITP electrolyte system and electrical decoupling between the focusing and sensing modes. Finally, we demonstrate an integrated device wherein the concentration enhancement due to ITP focusing leads to an increase in event rate of >300-fold in the ITP-NP device as compared to the NP-only case.
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Affiliation(s)
- Joshua D Spitzberg
- Department of Biomedical Engineering, The Technion - Israel Institute of Technology, Haifa, 32000 Israel.
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26
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Boobphahom S, Nguyet Ly M, Soum V, Pyun N, Kwon OS, Rodthongkum N, Shin K. Recent Advances in Microfluidic Paper-Based Analytical Devices toward High-Throughput Screening. Molecules 2020; 25:E2970. [PMID: 32605281 PMCID: PMC7412548 DOI: 10.3390/molecules25132970] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Microfluidic paper-based analytical devices (µPADs) have become promising tools offering various analytical applications for chemical and biological assays at the point-of-care (POC). Compared to traditional microfluidic devices, µPADs offer notable advantages; they are cost-effective, easily fabricated, disposable, and portable. Because of our better understanding and advanced engineering of µPADs, multistep assays, high detection sensitivity, and rapid result readout have become possible, and recently developed µPADs have gained extensive interest in parallel analyses to detect biomarkers of interest. In this review, we focus on recent developments in order to achieve µPADs with high-throughput capability. We discuss existing fabrication techniques and designs, and we introduce and discuss current detection methods and their applications to multiplexed detection assays in relation to clinical diagnosis, drug analysis and screening, environmental monitoring, and food and beverage quality control. A summary with future perspectives for µPADs is also presented.
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Affiliation(s)
- Siraprapa Boobphahom
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand;
| | - Mai Nguyet Ly
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Veasna Soum
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Nayoon Pyun
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Oh-Sun Kwon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Nadnudda Rodthongkum
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand;
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
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27
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Ouyang W, Han J. One‐Step Nucleic Acid Purification and Noise‐Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow‐Abundance Nucleic Acid Detection. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Wei Ouyang
- Department of Electrical Engineering and Computer Science and Research Laboratory of ElectronicsMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science and Research Laboratory of ElectronicsMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- Department of Biological EngineeringMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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28
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Ouyang W, Han J. One-Step Nucleic Acid Purification and Noise-Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow-Abundance Nucleic Acid Detection. Angew Chem Int Ed Engl 2020; 59:10981-10988. [PMID: 32246546 PMCID: PMC7560970 DOI: 10.1002/anie.201915788] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Indexed: 12/15/2022]
Abstract
Nucleic acid amplification tests (NAATs)integrated on a chip hold great promise for point-of-care diagnostics. Currently, nucleic acid (NA) purification remains time-consuming and labor-intensive, and it takes extensive efforts to optimize the amplification chemistry. Using selective electrokinetic concentration, we report one-step, liquid-phase NA purification that is simpler and faster than conventional solid-phase extraction. By further re-concentrating NAs and performing polymerase chain reaction (PCR) in a microfluidic chamber, our platform suppresses non-specific amplification caused by non-optimal PCR designs. We achieved the detection of 5 copies of M. tuberculosis genomic DNA (equaling 0.3 cell) in real biofluids using both optimized and non-optimal PCR designs, which is 10- and 1000-fold fewer than those of the standard bench-top method, respectively. By simplifying the workflow and shortening the development cycle of NAATs, our platform may find use in point-of-care diagnosis.
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Affiliation(s)
- Wei Ouyang
- Department of Electrical Engineering and Computer Science and Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science and Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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29
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Bender AT, Sullivan BP, Lillis L, Posner JD. Enzymatic and Chemical-Based Methods to Inactivate Endogenous Blood Ribonucleases for Nucleic Acid Diagnostics. J Mol Diagn 2020; 22:1030-1040. [PMID: 32450280 DOI: 10.1016/j.jmoldx.2020.04.211] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 01/28/2023] Open
Abstract
There are ongoing research efforts into simple and low-cost point-of-care nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. Herein, we investigate alternatives to standard guanidinium-based methods for RNase inactivation using an activity assay with an RNA substrate that fluoresces when cleaved. The effects of proteinase K, nonionic surfactants, SDS, dithiothreitol, and other additives on RNase activity in human serum are reported. Although proteinase K has been widely used in protocols for nuclease inactivation, it was found that high concentrations of proteinase K are unable to eliminate RNase activity in serum, unless used in concert with denaturing concentrations of SDS. It was observed that SDS must be combined with proteinase K, dithiothreitol, or both for irreversible and complete RNase inactivation in serum. This work provides an alternative chemistry for inactivating endogenous RNases for use in simple, low-cost point-of-care NATs for blood-borne pathogens.
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Affiliation(s)
- Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | | | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington; Department of Chemical Engineering, University of Washington, Seattle, Washington; Department of Family Medicine, University of Washington, Seattle, Washington.
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30
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Brunauer A, Ates HC, Dincer C, Früh SM. Integrated paper-based sensing devices for diagnostic applications. COMPREHENSIVE ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/bs.coac.2020.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Point-of-Care HIV Viral Load Testing: an Essential Tool for a Sustainable Global HIV/AIDS Response. Clin Microbiol Rev 2019; 32:32/3/e00097-18. [PMID: 31092508 DOI: 10.1128/cmr.00097-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The global public health community has set ambitious treatment targets to end the HIV/AIDS pandemic. With the notable absence of a cure, the goal of HIV treatment is to achieve sustained suppression of an HIV viral load, which allows for immunological recovery and reduces the risk of onward HIV transmission. Monitoring HIV viral load in people living with HIV is therefore central to maintaining effective individual antiretroviral therapy as well as monitoring progress toward achieving population targets for viral suppression. The capacity for laboratory-based HIV viral load testing has increased rapidly in low- and middle-income countries, but implementation of universal viral load monitoring is still hindered by several barriers and delays. New devices for point-of-care HIV viral load testing may be used near patients to improve HIV management by reducing the turnaround time for clinical test results. The implementation of near-patient testing using these new and emerging technologies may be an essential tool for ensuring a sustainable response that will ultimately enable an end to the HIV/AIDS pandemic. In this report, we review the current and emerging technology, the evidence for decentralized viral load monitoring by non-laboratory health care workers, and the additional considerations for expanding point-of-care HIV viral load testing.
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32
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Dong T, Wang GA, Li F. Shaping up field-deployable nucleic acid testing using microfluidic paper-based analytical devices. Anal Bioanal Chem 2019; 411:4401-4414. [DOI: 10.1007/s00216-019-01595-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/31/2018] [Accepted: 01/09/2019] [Indexed: 12/28/2022]
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33
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Ali Khan W, Yamini Y, Baharfar M, Balal Arain M. A new microfluidic-chip device for selective and simultaneous extraction of drugs with various properties. NEW J CHEM 2019. [DOI: 10.1039/c9nj01104h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the present study, a newly designed microfluidic-chip device was used for the selective and simultaneous electromembrane extraction (EME) of drugs with different properties.
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Affiliation(s)
- Wajid Ali Khan
- Department of Chemistry
- Faculty of Sciences
- Tarbiat Modares University
- Tehran
- Iran
| | - Yadollah Yamini
- Department of Chemistry
- Faculty of Sciences
- Tarbiat Modares University
- Tehran
- Iran
| | - Mahroo Baharfar
- Department of Chemistry
- Faculty of Sciences
- Tarbiat Modares University
- Tehran
- Iran
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34
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Christodouleas DC, Kaur B, Chorti P. From Point-of-Care Testing to eHealth Diagnostic Devices (eDiagnostics). ACS CENTRAL SCIENCE 2018; 4:1600-1616. [PMID: 30648144 PMCID: PMC6311959 DOI: 10.1021/acscentsci.8b00625] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Indexed: 05/09/2023]
Abstract
Point-of-care devices were originally designed to allow medical testing at or near the point of care by health-care professionals. Some point-of-care devices allow medical self-testing at home but cannot fully cover the growing diagnostic needs of eHealth systems that are under development in many countries. A number of easy-to-use, network-connected diagnostic devices for self-testing are needed to allow remote monitoring of patients' health. This Outlook highlights the essential characteristics of diagnostic devices for eHealth settings and indicates point-of-care technologies that may lead to the development of new devices. It also describes the most representative examples of simple-to-use, point-of-care devices that have been used for analysis of untreated biological samples.
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Affiliation(s)
| | - Balwinder Kaur
- Department of Chemistry, University
of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
| | - Parthena Chorti
- Department of Chemistry, University
of Massachusetts Lowell, Lowell, Massachusetts 01854, United States
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