1
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Zhong R, Sullivan M, Upreti N, Chen R, De Ganzó A, Yang K, Yang S, Jin K, He Y, Li K, Xia J, Ma Z, Lee LP, Konry T, Huang TJ. Cellular immunity analysis by a modular acoustofluidic platform: CIAMAP. SCIENCE ADVANCES 2023; 9:eadj9964. [PMID: 38134285 PMCID: PMC10745697 DOI: 10.1126/sciadv.adj9964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
The study of molecular mechanisms at the single-cell level holds immense potential for enhancing immunotherapy and understanding neuroinflammation and neurodegenerative diseases by identifying previously concealed pathways within a diverse range of paired cells. However, existing single-cell pairing platforms have limitations in low pairing efficiency, complex manual operation procedures, and single-use functionality. Here, we report a multiparametric cellular immunity analysis by a modular acoustofluidic platform: CIAMAP. This platform enables users to efficiently sort and collect effector-target (i.e., NK92-K562) cell pairs and monitor the real-time dynamics of immunological response formation. Furthermore, we conducted transcriptional and protein expression analyses to evaluate the pathways that mediate effector cytotoxicity toward target cells, as well as the synergistic effect of doxorubicin on the cellular immune response. Our CIAMAP can provide promising building blocks for high-throughput quantitative single-cell level coculture to understand intercellular communication while also empowering immunotherapy by precision analysis of immunological synapses.
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Affiliation(s)
- Ruoyu Zhong
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Matthew Sullivan
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Neil Upreti
- Biomedical Engineering Department, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Roy Chen
- Biomedical Engineering Department, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Agustin De Ganzó
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Kaichun Yang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Shujie Yang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ke Jin
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Ye He
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Ke Li
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Jianping Xia
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Zhiteng Ma
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Luke P. Lee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Tania Konry
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Tony Jun Huang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
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2
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Ho M, Sathishkumar N, Sklavounos AA, Sun J, Yang I, Nichols KP, Wheeler AR. Digital microfluidics with distance-based detection - a new approach for nucleic acid diagnostics. LAB ON A CHIP 2023; 24:63-73. [PMID: 37987330 DOI: 10.1039/d3lc00683b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
There is great enthusiasm for using loop-mediated isothermal amplification (LAMP) in point-of-care nucleic acid amplification tests (POC NAATs), as an alternative to PCR. While isothermal amplification techniques like LAMP eliminate the need for rapid temperature cycling in a portable format, these systems are still plagued by requirements for dedicated optical detection apparatus for analysis and manual off-chip sample processing. Here, we developed a new microfluidic system for LAMP-based POC NAATs to address these limitations. The new system combines digital microfluidics (DMF) with distance-based detection (DBD) for direct signal readout. This is the first report of the use of (i) LAMP or (ii) DMF with DBD - thus, we describe a number of characterization steps taken to determine optimal combinations of reagents, materials, and processes for reliable operation. For example, DBD was found to be quite sensitive to background signals from low molecular weight LAMP products; thus, a Capto™ adhere bead-based clean-up procedure was developed to isolate the desirable high-molecular-weight products for analysis. The new method was validated by application to detection of SARS-CoV-2 in saliva. The method was able to distinguish between saliva containing no virus, saliva containing a low viral load (104 genome copies per mL), and saliva containing a high viral load (108 copies per mL), all in an automated system that does not require detection apparatus for analysis. We propose that the combination of DMF with distance-based detection may be a powerful one for implementing a variety of POC NAATs or for other applications in the future.
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Affiliation(s)
- Man Ho
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - N Sathishkumar
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
| | - Ivy Yang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | | | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario, M5S 3H6, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
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3
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Coelho BJ, Pinto JV, Martins J, Rovisco A, Barquinha P, Fortunato E, Baptista PV, Martins R, Igreja R. Parylene C as a Multipurpose Material for Electronics and Microfluidics. Polymers (Basel) 2023; 15:polym15102277. [PMID: 37242852 DOI: 10.3390/polym15102277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Poly(p-xylylene) derivatives, widely known as Parylenes, have been considerably adopted by the scientific community for several applications, ranging from simple passive coatings to active device components. Here, we explore the thermal, structural, and electrical properties of Parylene C, and further present a variety of electronic devices featuring this polymer: transistors, capacitors, and digital microfluidic (DMF) devices. We evaluate transistors produced with Parylene C as a dielectric, substrate, and encapsulation layer, either semitransparent or fully transparent. Such transistors exhibit steep transfer curves and subthreshold slopes of 0.26 V/dec, negligible gate leak currents, and fair mobilities. Furthermore, we characterize MIM (metal-insulator-metal) structures with Parylene C as a dielectric and demonstrate the functionality of the polymer deposited in single and double layers under temperature and AC signal stimuli, mimicking the DMF stimuli. Applying temperature generally leads to a decrease in the capacitance of the dielectric layer, whereas applying an AC signal leads to an increase in said capacitance for double-layered Parylene C only. By applying the two stimuli, the capacitance seems to suffer from a balanced influence of both the separated stimuli. Lastly, we demonstrate that DMF devices with double-layered Parylene C allow for faster droplet motion and enable long nucleic acid amplification reactions.
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Affiliation(s)
- Beatriz J Coelho
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
- UCIBIO, I4HB, Department of Life Sciences, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Joana V Pinto
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Jorge Martins
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Ana Rovisco
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Pedro Barquinha
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Elvira Fortunato
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Pedro V Baptista
- UCIBIO, I4HB, Department of Life Sciences, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Rodrigo Martins
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
| | - Rui Igreja
- CENIMAT|i3N, Department of Materials Science, NOVA School of Science and Technology, Campus de Caparica, NOVA University of Lisbon and CEMOP/UNINOVA, 2829-516 Caparica, Portugal
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4
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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5
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Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
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Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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6
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Ho M, Au A, Flick R, Vuong TV, Sklavounos AA, Swyer I, Yip CM, Wheeler AR. Antifouling Properties of Pluronic and Tetronic Surfactants in Digital Microfluidics. ACS APPLIED MATERIALS & INTERFACES 2023; 15:6326-6337. [PMID: 36696478 DOI: 10.1021/acsami.2c17317] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fouling at liquid-solid interfaces is a pernicious problem for a wide range of applications, including those that are implemented by digital microfluidics (DMF). There are several strategies that have been used to combat surface fouling in DMF, the most common being inclusion of amphiphilic surfactant additives in the droplets to be manipulated. Initial studies relied on Pluronic additives, and more recently, Tetronic additives have been used, which has allowed manipulation of complex samples like serum and whole blood. Here, we report our evaluation of 19 different Pluronic and Tetronic additives, with attempts to determine (1) the difference in antifouling performance between the two families, (2) the structural similarities that predict exceptional antifouling performance, and (3) the mechanism of the antifouling behavior. Our analysis shows that both Pluronic and Tetronic additives with modest molar mass, poly(propylene oxide) (PPO) ≥50 units, poly(ethylene oxide) (PEO) mass percentage ≤50%, and hydrophilic-lipophilic balance (HLB) ca. 13-15 allow for exceptional antifouling performance in DMF. The most promising candidates, P104, P105, and T904, were able to support continuous movement of droplets of serum for more than 2 h, a result (for devices operating in air) previously thought to be out of reach for this technique. Additional results generated using device longevity assays, intrinsic fluorescence measurements, dynamic light scattering, asymmetric flow field flow fractionation, supercritical angle fluorescence microscopy, atomic force microscopy, and quartz crystal microbalance measurements suggest that the best-performing surfactants are more likely to operate by forming a protective layer at the liquid-solid interface than by complexation with proteins. We propose that these results and their implications are an important step forward for the growing community of users of this technique, which may provide guidance in selecting surfactants for manipulating biological matrices for a wide range of applications.
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Affiliation(s)
- Man Ho
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Aaron Au
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Robert Flick
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Thu V Vuong
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ian Swyer
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Christopher M Yip
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
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7
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Rutten I, Daems D, Leirs K, Lammertyn J. Highly Sensitive Multiplex Detection of Molecular Biomarkers Using Hybridization Chain Reaction in an Encoded Particle Microfluidic Platform. BIOSENSORS 2023; 13:100. [PMID: 36671935 PMCID: PMC9856145 DOI: 10.3390/bios13010100] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
In the continuous combat against diseases, there is the need for tools that enable an improved diagnostic efficiency towards higher information density combined with reduced time-to-result and cost. Here, a novel fully integrated microfluidic platform, the Evalution™, is evaluated as a potential solution to this need. Encoded microparticles combined with channel-based microfluidics allow a fast, sensitive and simultaneous detection of several disease-related biomarkers. Since the binary code is represented by physically present holes, 210 different codes can be created that will not be altered by light or chemically induced degradation. Exploiting the unique features of this multiplex platform, hybridization chain reaction (HCR) is explored as a generic approach to reach the desired sensitivity. Compared to a non-amplified reference system, the sensitivity was drastically improved by a factor of 104, down to low fM LOD values. Depending on the HCR duration, the assay can be tuned for sensitivity or total assay time, as desired. The huge potential of this strategy was further demonstrated by the successful detection of a multiplex panel of six different nucleic acid targets including viruses and bacteria. The ability to not only discriminate these two categories but, with the same effort, also virus strains (human adenovirus and human bocavirus), virus subtypes (human adenovirus type B and D) and antibiotic-resistant bacteria (Streptococcus pneumonia), exemplifies the specificity of the developed approach. The effective, yet highly simplified, isothermal and protein-enzyme-free signal amplification tool reaches an LOD ranging from as low as 33 ± 4 to 151 ± 12 fM for the different targets. Moreover, direct detection in a clinically relevant sample matrix was verified, resulting in a detection limit of 309 ± 80 fM, approximating the low fM levels detectable with the gold standard analysis method, PCR, without the drawbacks related to protein enzymes, thermal cycling and elaborate sample preparation steps. The reported strategy can be directly transferred as a generic approach for the sensitive and specific detection of various target molecules in multiplex. In combination with the high-throughput capacity and reduced reagent consumption, the Evalution™ demonstrates immense potential in the next generation of diagnostic tools towards more personalized medicine.
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8
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Huang C, Jiang Y, Li Y, Zhang H. Droplet Detection and Sorting System in Microfluidics: A Review. MICROMACHINES 2022; 14:mi14010103. [PMID: 36677164 PMCID: PMC9867185 DOI: 10.3390/mi14010103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 05/26/2023]
Abstract
Since being invented, droplet microfluidic technologies have been proven to be perfect tools for high-throughput chemical and biological functional screening applications, and they have been heavily studied and improved through the past two decades. Each droplet can be used as one single bioreactor to compartmentalize a big material or biological population, so millions of droplets can be individually screened based on demand, while the sorting function could extract the droplets of interest to a separate pool from the main droplet library. In this paper, we reviewed droplet detection and active sorting methods that are currently still being widely used for high-through screening applications in microfluidic systems, including the latest updates regarding each technology. We analyze and summarize the merits and drawbacks of each presented technology and conclude, with our perspectives, on future direction of development.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Yuqian Jiang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuwen Li
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77842, USA
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9
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Schmidt K, Hageneder S, Lechner B, Zbiral B, Fossati S, Ahmadi Y, Minunni M, Toca-Herrera JL, Reimhult E, Barisic I, Dostalek J. Rolling Circle Amplification Tailored for Plasmonic Biosensors: From Ensemble to Single-Molecule Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:55017-55027. [PMID: 36446038 PMCID: PMC9756284 DOI: 10.1021/acsami.2c14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
We report on the tailoring of rolling circle amplification (RCA) for affinity biosensors relying on the optical probing of their surface with confined surface plasmon field. Affinity capture of the target analyte at the metallic sensor surface (e.g., by using immunoassays) is followed by the RCA step for subsequent readout based on increased refractive index (surface plasmon resonance, SPR) or RCA-incorporated high number of fluorophores (in surface plasmon-enhanced fluorescence, PEF). By combining SPR and PEF methods, this work investigates the impact of the conformation of long RCA-generated single-stranded DNA (ssDNA) chains to the plasmonic sensor response enhancement. In order to confine the RCA reaction within the evanescent surface plasmon field and hence maximize the sensor response, an interface carrying analyte-capturing molecules and additional guiding ssDNA strands (complementary to the repeating segments of RCA-generated chains) is developed. When using the circular padlock probe as a model target analyte, the PEF readout shows that the reported RCA implementation improves the limit of detection (LOD) from 13 pM to high femtomolar concentration when compared to direct labeling. The respective enhancement factor is of about 2 orders of magnitude, which agrees with the maximum number of fluorophore emitters attached to the RCA chain that is folded in the evanescent surface plasmon field by the developed biointerface. Moreover, the RCA allows facile visualizing of individual binding events by fluorescence microscopy, which enables direct counting of captured molecules. This approach offers a versatile route toward a fast digital readout format of single-molecule detection with further reduced LOD.
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Affiliation(s)
- Katharina Schmidt
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST
Competence Center for Electrochemical Surface Technologies, 3430 Tulln an der
Donau, Austria
| | - Simone Hageneder
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Bernadette Lechner
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST
Competence Center for Electrochemical Surface Technologies, 3430 Tulln an der
Donau, Austria
| | - Barbara Zbiral
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Stefan Fossati
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Yasaman Ahmadi
- Molecular
Diagnostics, Health & Environment, AIT
Austrian Institute of Technology GmbH, 1210 Vienna, Austria
| | - Maria Minunni
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3-13, Sesto Fiorentino, 50019 Firenze, Italy
| | - Jose Luis Toca-Herrera
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Erik Reimhult
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Ivan Barisic
- Molecular
Diagnostics, Health & Environment, AIT
Austrian Institute of Technology GmbH, 1210 Vienna, Austria
| | - Jakub Dostalek
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- FZU-Institute
of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
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10
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Zhang T, Zhao W, Chen X, Zhang X, Zhu J, Li S, Wu C, Tian Z, Sui G. Fully Automated CRISPR-LAMP Platform for SARS-CoV-2 Delta and Omicron Variants. Anal Chem 2022; 94:15472-15480. [PMID: 36282886 DOI: 10.1021/acs.analchem.2c03607] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integrated clustered regularly interspaced short palindromic repeat (CRISPR)-loop-mediated amplification (LAMP) technology is of great importance in CRISPR-based diagnostic systems, which urgently needs to be developed to improve diagnostic accuracy. A labor-free, contamination-free, and fully automated droplet manipulation platform for the CRISPR-LAMP technology has not been developed before. Herein, we propose a fully automated CRISPR-LAMP platform, which can precisely manipulate the CRISPR-LAMP droplet and perform combined reactions with high sensitivity and specificity. SARS-CoV-2 Spike T478K, D614G, P681R, and P681H mutations, typical point mutations of B.1.617.2 (Delta) and Omicron variants, are monitored with this platform with a detection limit of 102 copies/μL. Allele discrimination between the mutants and wild type is significant with the designed one/two-mismatch CRISPR RNA (crRNA) at a limit of 102 copies/μL. Chemically synthesized and modified crRNAs greatly increase the CRISPR-LAMP signal, which advance the wide application. Combined with the previously developed RdRp CRISPR-LAMP assay, clinical results showed that Spike T478K and P681H can discriminate the mutant type form the wild type with 70% (49.66-85.50%, 95% confidence interval) and 78% (57.27-90.62%, 95% confidence interval) sensitivity, respectively, and 100% specificity (51.68-100%, 95% confidence interval), and the RdRp target can detect SARS-CoV-2 strains with 85% sensitivity (65.39-95.14%, 95% confidence interval) and 100% specificity (51.68-100%, 95% confidence interval). We believe that this automatic digital microfluid (DMF) system can advance the integrated CRISPR-LAMP technology with higher stability, sensitivity, and practicability, also for other CRISPR-associated diagnostic platforms.
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Affiliation(s)
- Tong Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Xi Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Xinlian Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Jinhui Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center (Shanghai Customs Port Clinic), 2090 Jinqiao Road, Shanghai 200433, P. R. China
| | - Chuanyong Wu
- Shanghai Hengxin BioTechnology, 1688 North Guo Quan Road, Bldg A8, Rm 801, Shanghai 200438, P. R. China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center (Shanghai Customs Port Clinic), 2090 Jinqiao Road, Shanghai 200433, P. R. China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, P. R. China
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CICAEET), Nanjing University of Information Science & Technology, Nanjing 210044, P. R. China
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11
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Shen R, Lv A, Yi S, Wang P, Mak PI, Martins RP, Jia Y. Nucleic acid analysis on electrowetting-based digital microfluidics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Soares RRG, Madaboosi N, Nilsson M. Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping. Acc Chem Res 2021; 54:3979-3990. [PMID: 34637281 PMCID: PMC8567418 DOI: 10.1021/acs.accounts.1c00438] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of robust methods allowing the precise detection of specific nucleic acid sequences is of major societal relevance, paving the way for significant advances in biotechnology and biomedical engineering. These range from a better understanding of human disease at a molecular level, allowing the discovery and development of novel biopharmaceuticals and vaccines, to the improvement of biotechnological processes providing improved food quality and safety, efficient green fuels, and smart textiles. Among these applications, the significance of pathogen diagnostics as the main focus of this Account has become particularly clear during the recent SARS-CoV-2 pandemic. In this context, while RT-PCR is the gold standard method for unambiguous detection of genetic material from pathogens, other isothermal amplification alternatives circumventing rapid heating-cooling cycles up to ∼95 °C are appealing to facilitate the translation of the assay into point-of-care (PoC) analytical platforms. Furthermore, the possibility of routinely multiplexing the detection of tens to hundreds of target sequences with single base pair specificity, currently not met by state-of-the-art methods available in clinical laboratories, would be instrumental along the path to tackle emergent viral variants and antimicrobial resistance genes. Here, we advocate that padlock probes (PLPs), first reported by Nilsson et al. in 1994, coupled with rolling circle amplification (RCA), termed here as PLP-RCA, is an underexploited technology in current arena of isothermal nucleic acid amplification tests (NAATs) providing an unprecedented degree of multiplexing, specificity, versatility, and amenability to integration in miniaturized PoC platforms. Furthermore, the intrinsically digital amplification of PLP-RCA retains spatial information and opens new avenues in the exploration of pathogenesis with spatial multiomics analysis of infected cells and tissue.The Account starts by introducing PLP-RCA in a nutshell focusing individually on the three main assay steps, namely, (1) PLP design and ligation mechanism, (2) RCA after probe ligation, and (3) detection of the RCA products. Each subject is touched upon succinctly but with sufficient detail for the reader to appreciate some assay intricacies and degree of versatility depending on the analytical challenge at hand. After familiarizing the reader with the method, we discuss specific examples of research in our group and others using PLP-RCA for viral, bacterial, and fungal diagnostics in a variety of clinical contexts, including the genotyping of antibiotic resistance genes and viral subtyping. Then, we dissect key developments in the miniaturization and integration of PLP-RCA to minimize user input, maximize analysis throughput, and expedite the time to results, ultimately aiming at PoC applications. These developments include molecular enrichment for maximum sensitivity, spatial arrays to maximize analytical throughput, automation of liquid handling to streamline the analytical workflow in miniaturized devices, and seamless integration of signal transduction to translate RCA product titers (and ideally spatial information) into a readable output. Finally, we position PLP-RCA in the current landscape of NAATs and furnish a systematic Strengths, Weaknesses, Opportunities and Threats analysis to shine light upon unpolished edges to uncover the gem with potential for ubiquitous, precise, and unbiased pathogen diagnostics.
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Affiliation(s)
- Ruben R. G. Soares
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
- Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, 17165 Solna, Sweden
| | - Narayanan Madaboosi
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036 Tamil Nadu, India
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
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13
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Alidoust M, Baharfar M, Manouchehri M, Yamini Y, Tajik M, Seidi S. Emergence of microfluidic devices in sample extraction; an overview of diverse methodologies, principals, and recent advancements. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Perry JM, Soffer G, Jain R, Shih SCC. Expanding the limits towards 'one-pot' DNA assembly and transformation on a rapid-prototype microfluidic device. LAB ON A CHIP 2021; 21:3730-3741. [PMID: 34369550 DOI: 10.1039/d1lc00415h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
DNA assembly and transformation are crucial to the building process in synthetic biology. These steps are significant roadblocks when engineering increasingly complex biological systems. To address this, recent development of widespread 'biofoundry' facilities has employed automation equipment to expedite the synthetic biology workflow. Despite significant progress, there is a clear demand for lower-cost and smaller-footprint automation equipment. The field of microfluidics have emerged to provide automation capabilities to meet this demand. However, we still lack devices capable of building large multi-gene systems in a consolidated process. In response to this challenge, we have developed a digital microfluidic platform that performs "one-pot" Golden Gate DNA assembly of large plasmids and transformation of E coli. The system features a novel electrode geometry and modular design, which make these devices simple to fabricate and use, thus improving the accessibility of microfluidics. This device incorporates an impedance-based adaptive closed loop water replenishment system to compensate for droplet evaporation and maintain constant assembly reaction concentrations, which we found to be crucial to the DNA assembly efficiency. We also showcase a closed-loop temperature control system that generates precise thermodynamic profiles to optimize heat shock transformation. Moreover, we validated the system by assembling and transforming large and complex plasmids conferring a biosynthetic pathway, resulting in performance comparable to those of standard techniques. We propose that the methods described here will contribute to a new generation of accessible automation platforms aimed at speeding up the 'building' process, lowering reagent consumption and removing manual work from synthetic biology.
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Affiliation(s)
- James M Perry
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
| | - Guy Soffer
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Raja Jain
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
| | - Steve C C Shih
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
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15
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Cai K, Mankar S, Ajiri T, Shirai K, Yotoriyama T. An integrated high-throughput microfluidic circulatory fluorescence-activated cell sorting system (μ-CFACS) for the enrichment of rare cells. LAB ON A CHIP 2021; 21:3112-3127. [PMID: 34286793 DOI: 10.1039/d1lc00298h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
There is an increasing need for the enrichment of rare cells in the clinical environments of precision medicine, personalized medicine, and regenerative medicine. With the possibility of becoming the next-generation cell sorters, microfluidic fluorescence-activated cell sorting (μ-FACS) devices have been developed to avoid cross-contamination, minimize device footprint, and eliminate bio-aerosols. However, due to highly precise flow control, the achievable throughput of the μ-FACS system is generally lower than the throughput of conventional FACS devices. Here, we report a fully integrated high-throughput microfluidic circulatory fluorescence-activated cell sorting (μ-CFACS) system for the enrichment of clinical rare cells. A microfluidic sorting cartridge has been developed for enriching samples through a sequential sorting process, which was further realized by the integration of both fast amplified piezoelectrically actuated on-chip valves and compact pneumatic cylinders actuated on-chip valves. At an equivalent throughput of ∼8000 events per second (eps), the purity of rare fluorescent microparticles has been significantly increased from ∼0.01% to ∼27.97%. An enrichment of ∼9400-fold from 0.009% to 81.86% has also been demonstrated for isolating fluorescently labelled MCF-7 breast cancer cells from Jurkat cells at an equivalent sorting throughput of ∼6400 eps. With the advantages of high throughput and contamination-free design, the proposed integrated μ-CFACS system provides a new option for the enrichment of clinical rare cells.
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Affiliation(s)
- Kunpeng Cai
- Central Research Laboratories, Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan.
| | - Shruti Mankar
- Central Research Laboratories, Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan.
| | - Taiga Ajiri
- Central Research Laboratories, Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan.
| | - Kentaro Shirai
- Central Research Laboratories, Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan.
| | - Tasuku Yotoriyama
- Central Research Laboratories, Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe 651-2271, Japan.
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16
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You M, Peng P, Xue Z, Tong H, He W, Mao P, Liu Q, Yao C, Xu F. A fast and ultrasensitive ELISA based on rolling circle amplification. Analyst 2021; 146:2871-2877. [PMID: 33899835 DOI: 10.1039/d1an00355k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A highly sensitive ELISA is critical for early diagnosis and biomarker discovery of various diseases. Although various ELISA technologies have been developed with high sensitivity, they are limited by poor repeatability, high cost, the dependence on complex equipment and/or a prolonged reaction time. To this end, we developed a fast and ultrasensitive ELISA (termed RELISA) based on rolling circle amplification (RCA) and enzymatic signal amplification. The RELISA is established on the traditional ELISA, with only one more RCA step that can be accomplished within 10 minutes. The prolonged single strand DNA (ssDNA) from RCA is able to enrich abundant horseradish peroxidase conjugate (HRP) modified detection probes. Consequently, the intensive HRP is able to catalyze TMB-H2O2 to produce significantly enhanced colorimetric signals. With CEACAM-7 as a model biomarker, the RELISA achieves the limit of detection as low as 2.82 pg mL-1, which is ∼50 times higher than that of the traditional ELISA. Therefore, we envision that the developed RELISA would be a powerful tool for the early diagnosis of various major diseases.
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Affiliation(s)
- Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Ping Peng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China and Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China.
| | - Zhenrui Xue
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China and Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China.
| | - Haoyang Tong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Wanghong He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China and Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Ping Mao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China and Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China.
| | - Qi Liu
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China.
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China. and State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China. and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
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17
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Cai K, Mankar S, Maslova A, Ajiri T, Yotoriyama T. Amplified piezoelectrically actuated on-chip flow switching for a rapid and stable microfluidic fluorescence activated cell sorter. RSC Adv 2020; 10:40395-40405. [PMID: 35520855 PMCID: PMC9057478 DOI: 10.1039/d0ra04919k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/25/2020] [Indexed: 01/22/2023] Open
Abstract
With the potential to avoid cross-contamination, eliminate bio-aerosols, and minimize device footprints, microfluidic fluorescence-activated cell sorting (μ-FACS) devices could become the platform for the next generation cell sorter. Here, we report an on-chip flow switching based μ-FACS mechanism with piezoelectric actuation as a fast and robust sorting solution. A microfluidic chip with bifurcate configuration and displacement amplified piezoelectric microvalves has been developed to build the μ-FACS system. Rare fluorescent microparticles of different sizes have been significantly enriched from a purity of ∼0.5% to more than 90%. An enrichment of 150-fold from ∼0.6% to ∼91% has also been confirmed for fluorescently labeled MCF-7 breast cancer cells from Jurkat cells, while viability after sorting was maintained. Taking advantage of its simple structure, low cost, fast response, and reliable flow regulation, the proposed μ-FACS system delivers a new option that can meet the requirements of sorting performance, target selectivity, device lifetime, and cost-effectiveness of implementation.
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Affiliation(s)
- Kunpeng Cai
- Central Research Laboratories, Sysmex Corporation 4-4-4 Takatsukadai, Nishi-ku Kobe 651-2271 Japan
| | - Shruti Mankar
- Central Research Laboratories, Sysmex Corporation 4-4-4 Takatsukadai, Nishi-ku Kobe 651-2271 Japan
| | - Anastasia Maslova
- Central Research Laboratories, Sysmex Corporation 4-4-4 Takatsukadai, Nishi-ku Kobe 651-2271 Japan
| | - Taiga Ajiri
- Central Research Laboratories, Sysmex Corporation 4-4-4 Takatsukadai, Nishi-ku Kobe 651-2271 Japan
| | - Tasuku Yotoriyama
- Central Research Laboratories, Sysmex Corporation 4-4-4 Takatsukadai, Nishi-ku Kobe 651-2271 Japan
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18
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Kothamachu VB, Zaini S, Muffatto F. Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable. SLAS Technol 2020; 25:411-426. [PMID: 32584152 DOI: 10.1177/2472630320931794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner. This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments. Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays. These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules. In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data. In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework.
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19
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Tian B, Gao F, Fock J, Dufva M, Hansen MF. Homogeneous circle-to-circle amplification for real-time optomagnetic detection of SARS-CoV-2 RdRp coding sequence. Biosens Bioelectron 2020; 165:112356. [PMID: 32510339 DOI: 10.1016/j.bios.2020.112356] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Circle-to-circle amplification (C2CA) is a specific and precise cascade nucleic acid amplification method consisting of more than one round of padlock probe ligation and rolling circle amplification (RCA). Although C2CA provides a high amplification efficiency with a negligible increase of false-positive risk, it contains several step-by-step operation processes. We herein demonstrate a homogeneous and isothermal nucleic acid quantification strategy based on C2CA and optomagnetic analysis of magnetic nanoparticle (MNP) assembly. The proposed homogeneous circle-to-circle amplification eliminates the need for additional monomerization and ligation steps after the first round of RCA, and combines two amplification rounds in a one-pot reaction. The second round of RCA produces amplicon coils that anneal to detection probes grafted onto MNPs, resulting in MNP assembly that can be detected in real-time using an optomagnetic sensor. The proposed methodology was applied for the detection of a synthetic complementary DNA of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2, also known as 2019-nCoV) RdRp (RNA-dependent RNA polymerase) coding sequence, achieving a detection limit of 0.4 fM with a dynamic detection range of 3 orders of magnitude and a total assay time of ca. 100 min. A mathematical model was set up and validated to predict the assay performance. Moreover, the proposed method was specific to distinguish SARS-CoV and SARS-CoV-2 sequences with high similarity.
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Affiliation(s)
- Bo Tian
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800, Kongens Lyngby, Denmark.
| | - Fei Gao
- Department of Physics, Technical University of Denmark, DTU Physics, Building 307, DK-2800, Kongens Lyngby, Denmark
| | - Jeppe Fock
- Blusense Diagnostics ApS, Fruebjergvej 3, DK-2100, Copenhagen, Denmark
| | - Martin Dufva
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800, Kongens Lyngby, Denmark
| | - Mikkel Fougt Hansen
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800, Kongens Lyngby, Denmark.
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Guo J, Lin L, Zhao K, Song Y, Huang M, Zhu Z, Zhou L, Yang C. Auto-affitech: an automated ligand binding affinity evaluation platform using digital microfluidics with a bidirectional magnetic separation method. LAB ON A CHIP 2020; 20:1577-1585. [PMID: 32207498 DOI: 10.1039/d0lc00024h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The dissociation constant (Kd) is a crucial parameter for characterizing binding affinity in molecular recognition, including antigen-antibody, DNA-protein, and receptor-ligand interactions. However, conventional methods for Kd characterization usually involve a multi-step process and time-consuming operations for incubation, washing, and detection, thus causing problems, such as time delays, microbead loss, degradation of sensitive molecules, and personal errors. Here we demonstrate an automated ligand binding affinity evaluation platform (Auto-affitech) using digital microfluidics (DMF), with individual droplets at the microliter level, programmed to rapidly perform the incubation and separation of target-beads and binding ligands. Because the loss of the beads influences the detection results, we propose a new strategy for magnetic bead separation using DMF, termed the bidirectional separation method. By splitting one droplet into two asymmetric droplets, high bead retention efficiency (89.57% ± 0.05%) and high washing efficiency (99.59% ± 0.17%, with four washings) were obtained. We demonstrate the determination of Kd of an aptamer-protein system (EpCAM and its corresponding aptamer SYL3C) and an antigen-antibody system (H5N1 antigen and antibody), proving the capability and universality of Auto-affitech in various receptor-ligand systems. Integrating all the sample processing procedures, the Auto-affitech not only saves manual labor and minimizes personal errors, but also conserves samples and shortens analysis time. Overall, this platform successfully demonstrates to be an automated approach for dissociation constant evaluation and exhibits great potential for highly efficient screening of ligands.
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Affiliation(s)
- Jingjing Guo
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Li Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Kaifeng Zhao
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mengjiao Huang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Leiji Zhou
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Chaoyong Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China. and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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Ciftci S, Neumann F, Abdurahman S, Appelberg KS, Mirazimi A, Nilsson M, Madaboosi N. Digital Rolling Circle Amplification-Based Detection of Ebola and Other Tropical Viruses. J Mol Diagn 2020; 22:272-283. [PMID: 31837428 DOI: 10.1016/j.jmoldx.2019.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 09/04/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
Emerging tropical viruses have caused serious outbreaks during the recent years, such as Ebola virus (EBOV) in 2014 and the most recent in 2018 to 2019 in Congo. Thus, immediate diagnostic attention is demanded at the point of care in resource-limited settings, because the performance and the operational parameters of conventional EBOV testing are limited. Especially, their sensitivity, specificity, and coverage of other tropical disease viruses make them unsuitable for diagnostic at the point of care. Here, a padlock probe (PLP)-based rolling circle amplification (RCA) method for the detection of EBOV is presented. For this, a set of PLPs, separately targeting the viral RNA and complementary RNA of all seven EBOV genes, was used in the RCA assay and validated on virus isolates from cell culture. The assay was then translated for testing clinical samples, and simultaneous detection of both EBOV RNA types was demonstrated. For increased sensitivity, the RCA products were enriched on a simple and pump-free microfluidic chip. Because PLPs and RCA are inherently multiplexable, we demonstrate the extension of the probe panel for the simultaneous detection of the tropical viruses Ebola, Zika, and Dengue. The demonstrated high specificity, sensitivity, and multiplexing capability in combination with the digital quantification rendered the assay a promising diagnostic tool toward tropical virus detection at the point of care.
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Affiliation(s)
- Sibel Ciftci
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Felix Neumann
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | | | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden; LABMED, Karolinska Institute and Karolinska Hospital University, Solna, Sweden; National Veterinary Institute, Uppsala, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
| | - Narayanan Madaboosi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
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22
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Martorell S, Tortajada-Genaro LA, Maquieira Á. Magnetic concentration of allele-specific products from recombinase polymerase amplification. Anal Chim Acta 2019; 1092:49-56. [DOI: 10.1016/j.aca.2019.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/06/2019] [Indexed: 02/07/2023]
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Leipert J, Tholey A. Miniaturized sample preparation on a digital microfluidics device for sensitive bottom-up microproteomics of mammalian cells using magnetic beads and mass spectrometry-compatible surfactants. LAB ON A CHIP 2019; 19:3490-3498. [PMID: 31531506 DOI: 10.1039/c9lc00715f] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
While LC-MS-based proteomics with high nanograms to micrograms of total protein has become routine, the analysis of samples derived from low cell numbers is challenged by factors such as sample losses, or difficulties encountered with the manual manipulation of small liquid volumes. Digital microfluidics (DMF) is an emerging technique for miniaturized and automated droplet manipulation, which has been proposed as a promising tool for proteomic sample preparation. However, proteome analysis of samples prepared on-chip by DMF has previously been unfeasible, due to incompatibility with down-stream LC-MS instrumentation. To overcome these limitations, we here developed protocols for bottom-up LC-MS based proteomics sample preparation of as little as 100 mammalian cells on a commercially available digital microfluidics device. To this end, we developed effective cell lysis conditions optimized for DMF, as well as detergent-buffer systems compatible with downstream proteolytic digestion on DMF chips and subsequent LC-MS analysis. A major step was the introduction of the single-pot, solid-phase-enhanced sample preparation (SP3) approach on-chip, which allowed the removal of salts and anti-fouling polymeric detergents, thus rendering sample preparation by DMF compatible with LC-MS-based proteome analysis. Application of DMF-SP3 to the proteome analysis of Jurkat T cells led to the identification of up to 2500 proteins from approximately 500 cells, and up to 1200 proteins from approximately 100 cells on an Orbitrap mass spectrometer, emphasizing the high compatibility of DMF-SP3 with low protein input and minute volumes handled by DMF. Taken together, we demonstrate the first sample preparation workflow for proteomics on a DMF chip device reported so far, allowing the sensitive analysis of limited biological material.
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Affiliation(s)
- Jan Leipert
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany.
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24
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Daems D, Rutten I, Bath J, Decrop D, Van Gorp H, Ruiz EP, De Feyter S, Turberfield AJ, Lammertyn J. Controlling the Bioreceptor Spatial Distribution at the Nanoscale for Single Molecule Counting in Microwell Arrays. ACS Sens 2019; 4:2327-2335. [PMID: 31436077 DOI: 10.1021/acssensors.9b00877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The ability to detect low concentrations of protein biomarkers is crucial for the early-stage detection of many diseases and therefore indispensable for improving diagnostic devices for healthcare. Here, we demonstrate that by integrating DNA nanotechnologies like DNA origami and aptamers, we can design innovative biosensing concepts for reproducible and sensitive detection of specific targets. DNA origami structures decorated with aptamers were studied as a novel tool to structure the biosensor surface with nanoscale precision in a digital detection bioassay, enabling control of the density, orientation, and accessibility of the bioreceptor to optimize the interaction between target and aptamer. DNA origami was used to control the spatial distribution of an in-house-generated aptamer on superparamagnetic microparticles, resulting in an origami-linked digital aptamer bioassay to detect the main peanut antigen Ara h1 with 2-fold improved signal-to-noise ratio and 15-fold improved limit of detection compared to a digital bioassay without DNA origami. Moreover, the sensitivity achieved was 4 orders of magnitude higher than commercially available and literature-reported enzyme-linked immunosorbent assay techniques. In conclusion, this novel and innovative approach to engineer biosensing interfaces will be of major interest to scientists and clinicians looking for new molecular insights and ultrasensitive detection of a broad range of targets, and, for the next generation of diagnostics.
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Affiliation(s)
- Devin Daems
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Iene Rutten
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Jonathan Bath
- Department of Physics, Clarendon Laboratory, Oxford University, Parks Road, Oxford OX1 3PU, U.K
| | - Deborah Decrop
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Hans Van Gorp
- Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200f, B-3001 Leuven, Belgium
| | - Elena Pérez Ruiz
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
| | - Steven De Feyter
- Department of Chemistry, Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200f, B-3001 Leuven, Belgium
| | - Andrew J. Turberfield
- Department of Physics, Clarendon Laboratory, Oxford University, Parks Road, Oxford OX1 3PU, U.K
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
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25
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26
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Minero GAS, Cangiano V, Garbarino F, Fock J, Hansen MF. Integration of microbead DNA handling with optomagnetic detection in rolling circle amplification assays. Mikrochim Acta 2019; 186:528. [DOI: 10.1007/s00604-019-3636-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/25/2019] [Indexed: 01/14/2023]
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27
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Jiang Y, Li S, Qiu Z, Le T, Zou S, Cao X. Rolling circle amplification and its application in microfluidic systems for
Escherichia coli
O157:H7 detections. J Food Saf 2019. [DOI: 10.1111/jfs.12671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Yuqian Jiang
- Department of Chemical and Biological EngineeringUniversity of Ottawa Ottawa Ontario Canada
- Measurement Science and StandardsNational Research Council Canada Ottawa Ontario Canada
| | - Shuying Li
- Department of Chemical and Biological EngineeringUniversity of Ottawa Ottawa Ontario Canada
- Measurement Science and StandardsNational Research Council Canada Ottawa Ontario Canada
| | - Zhenyu Qiu
- Division of Advanced FabricationsNanchang Institute of Technology Nanchang Jiangxi Province China
| | - Tao Le
- College of Life ScienceChongqing Normal University Shapingba Chongqing China
| | - Shan Zou
- Measurement Science and StandardsNational Research Council Canada Ottawa Ontario Canada
| | - Xudong Cao
- Department of Chemical and Biological EngineeringUniversity of Ottawa Ottawa Ontario Canada
- Ottawa‐Carleton Institute of Biomedical EngineeringUniversity of Ottawa Ottawa Ontario Canada
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28
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LampPort: a handheld digital microfluidic device for loop-mediated isothermal amplification (LAMP). Biomed Microdevices 2019; 21:9. [DOI: 10.1007/s10544-018-0354-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Neumann F, Hernández-Neuta I, Grabbe M, Madaboosi N, Albert J, Nilsson M. Padlock Probe Assay for Detection and Subtyping of Seasonal Influenza. Clin Chem 2018; 64:1704-1712. [PMID: 30257827 DOI: 10.1373/clinchem.2018.292979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/31/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Influenza remains a constant threat worldwide, and WHO estimates that it affects 5% to 15% of the global population each season, with an associated 3 to 5 million severe cases and up to 500000 deaths. To limit the morbidity and the economic burden of influenza, improved diagnostic assays are needed. METHODS We developed a multiplexed assay for the detection and subtyping of seasonal influenza based on padlock probes and rolling circle amplification. The assay simultaneously targets all 8 genome segments of the 4 circulating influenza variants-A(H1N1), A(H3N2), B/Yamagata, and B/Victoria-and was combined with a prototype cartridge for inexpensive digital quantification. Characterized virus isolates and patient nasopharyngeal swabs were used for assay design and analytical validation. The diagnostic performance was assessed by blinded testing of 50 clinical samples analyzed in parallel with a commercial influenza assay, Simplexa™ Flu A/B & RSV Direct. RESULTS The assay had a detection limit of 18 viral RNA copies and achieved 100% analytical and clinical specificity for differential detection and subtyping of seasonal circulating influenza variants. The diagnostic sensitivity on the 50 clinical samples was 77.5% for detecting influenza and up to 73% for subtyping seasonal variants. CONCLUSIONS We have presented a proof-of-concept padlock probe assay combined with an inexpensive digital readout for the detection and subtyping of seasonal influenza strains A and B. The demonstrated high specificity and multiplexing capability, together with the digital quantification, established the assay as a promising diagnostic tool for seasonal influenza.
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Affiliation(s)
- Felix Neumann
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Iván Hernández-Neuta
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Malin Grabbe
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Narayanan Madaboosi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden;
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30
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Microfluidic magnetic fluidized bed for DNA analysis in continuous flow mode. Biosens Bioelectron 2018; 102:531-539. [DOI: 10.1016/j.bios.2017.11.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/25/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022]
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31
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Sepehri S, Eriksson E, Kalaboukhov A, Zardán Gómez de la Torre T, Kustanovich K, Jesorka A, Schneiderman JF, Blomgren J, Johansson C, Strømme M, Winkler D. Volume-amplified magnetic bioassay integrated with microfluidic sample handling and high- Tc SQUID magnetic readout. APL Bioeng 2017; 2:016102. [PMID: 31069287 PMCID: PMC6481700 DOI: 10.1063/1.4999713] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/26/2017] [Indexed: 11/14/2022] Open
Abstract
A bioassay based on a high-Tc superconducting quantum interference device (SQUID) reading out functionalized magnetic nanoparticles (fMNPs) in a prototype microfluidic platform is presented. The target molecule recognition is based on volume amplification using padlock-probe-ligation followed by rolling circle amplification (RCA). The MNPs are functionalized with single-stranded oligonucleotides, which give a specific binding of the MNPs to the large RCA coil product, resulting in a large change in the amplitude of the imaginary part of the ac magnetic susceptibility. The RCA products from amplification of synthetic Vibrio cholera target DNA were investigated using our SQUID ac susceptibility system in microfluidic channel with an equivalent sample volume of 3 μl. From extrapolation of the linear dependence of the SQUID signal versus concentration of the RCA coils, it is found that the projected limit of detection for our system is about 1.0 × 105 RCA coils (0.2 × 10−18 mol), which is equivalent to 66 fM in the 3 μl sample volume. This ultra-high magnetic sensitivity and integration with microfluidic sample handling are critical steps towards magnetic bioassays for rapid detection of DNA and RNA targets at the point of care.
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Affiliation(s)
- Sobhan Sepehri
- Department of Microtechnology and Nanoscience-MC2, Chalmers University of Technology, Göteborg 412 96, Sweden
| | | | - Alexei Kalaboukhov
- Department of Microtechnology and Nanoscience-MC2, Chalmers University of Technology, Göteborg 412 96, Sweden
| | | | - Kiryl Kustanovich
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg 412 96, Sweden
| | - Aldo Jesorka
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg 412 96, Sweden
| | | | | | | | - Maria Strømme
- Department of Engineering Sciences, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
| | - Dag Winkler
- Department of Microtechnology and Nanoscience-MC2, Chalmers University of Technology, Göteborg 412 96, Sweden
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32
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Serra M, Ferraro D, Pereiro I, Viovy JL, Descroix S. The power of solid supports in multiphase and droplet-based microfluidics: towards clinical applications. LAB ON A CHIP 2017; 17:3979-3999. [PMID: 28948991 DOI: 10.1039/c7lc00582b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Multiphase and droplet microfluidic systems are growing in relevance in bioanalytical-related fields, especially due to the increased sensitivity, faster reaction times and lower sample/reagent consumption of many of its derived bioassays. Often applied to homogeneous (liquid/liquid) reactions, innovative strategies for the implementation of heterogeneous (typically solid/liquid) processes have recently been proposed. These involve, for example, the extraction and purification of target analytes from complex matrices or the implementation of multi-step protocols requiring efficient washing steps. To achieve this, solid supports such as functionalized particles (micro or nanometric) presenting different physical properties (e.g. magnetic, optical or others) are used for the binding of specific entities. The manipulation of such supports with different microfluidic principles has both led to the miniaturization of existing biomedical protocols and the development of completely new strategies for diagnostics and research. In this review, multiphase and droplet-based microfluidic systems using solid suspensions are presented and discussed with a particular focus on: i) working principles and technological developments of the manipulation strategies and ii) applications, critically discussing the level of maturity of these systems, which can range from initial proofs of concept to real clinical validations.
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Affiliation(s)
- M Serra
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.
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33
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A Digital Microfluidics Platform for Loop-Mediated Isothermal Amplification Detection. SENSORS 2017; 17:s17112616. [PMID: 29144379 PMCID: PMC5713054 DOI: 10.3390/s17112616] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/31/2017] [Accepted: 11/10/2017] [Indexed: 12/18/2022]
Abstract
Digital microfluidics (DMF) arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP), allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC), providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities. Here, we demonstrate for the first time the role of coupling DMF and LAMP, in a dedicated device that allows straightforward mixing of LAMP reagents and target DNA, as well as optimum temperature control (reaction droplets undergo a temperature variation of just 0.3 °C, for 65 °C at the bottom plate). This device is produced using low-temperature and low-cost production processes, adaptable to disposable and flexible substrates. DMF-LAMP is performed with enhanced sensitivity without compromising reaction efficacy or losing reliability and efficiency, by LAMP-amplifying 0.5 ng/µL of target DNA in just 45 min. Moreover, on-chip LAMP was performed in 1.5 µL, a considerably lower volume than standard bench-top reactions.
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34
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Digital Microfluidics for Nucleic Acid Amplification. SENSORS 2017; 17:s17071495. [PMID: 28672827 PMCID: PMC5539496 DOI: 10.3390/s17071495] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/17/2017] [Accepted: 06/22/2017] [Indexed: 01/08/2023]
Abstract
Digital Microfluidics (DMF) has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.
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35
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Tangchaikeeree T, Polpanich D, Elaissari A, Jangpatarapongsa K. Magnetic particles for in vitro molecular diagnosis: From sample preparation to integration into microsystems. Colloids Surf B Biointerfaces 2017; 158:1-8. [PMID: 28654866 DOI: 10.1016/j.colsurfb.2017.06.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/05/2017] [Accepted: 06/19/2017] [Indexed: 12/16/2022]
Abstract
Colloidal magnetic particles (MPs) have been developed in association with molecular diagnosis for several decades. MPs have the great advantage of easy manipulation using a magnet. In nucleic acid detection, these particles can act as a capture support for rapid and simple biomolecule separation. The surfaces of MPs can be modified by coating with various polymer materials to provide functionalization for different applications. The use of MPs enhances the sensitivity and specificity of detection due to the specific activity on the surface of the particles. Practical applications of MPs demonstrate greater efficiency than conventional methods. Beyond traditional detection, MPs have been successfully adopted as a smart carrier in microfluidic and lab-on-a-chip biosensors. The versatility of MPs has enabled their integration into small single detection units. MPs-based biosensors can facilitate rapid and highly sensitive detection of very small amounts of a sample. In this review, the application of MPs to the detection of nucleic acids, from sample preparation to analytical readout systems, is described. State-of-the-art integrated microsystems containing microfluidic and lab-on-a-chip biosensors for the nucleic acid detection are also addressed.
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Affiliation(s)
- Tienrat Tangchaikeeree
- University Lyon-1, CNRS, LAGEP UMR 5007,43 Boulevard du 11 Novembre 1918, 69100, Villeurbanne, France; Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Duangporn Polpanich
- National Nanotechnology Center, National Science and Technology Development Agency (NSTDA),130 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Abdelhamid Elaissari
- University Lyon-1, CNRS, LAGEP UMR 5007,43 Boulevard du 11 Novembre 1918, 69100, Villeurbanne, France
| | - Kulachart Jangpatarapongsa
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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36
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Giuffrida MC, Spoto G. Integration of isothermal amplification methods in microfluidic devices: Recent advances. Biosens Bioelectron 2017; 90:174-186. [DOI: 10.1016/j.bios.2016.11.045] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 01/02/2023]
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37
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Sarkar S, Sabhachandani P, Konry T. Isothermal Amplification Strategies for Detection in Microfluidic Devices. Trends Biotechnol 2017; 35:186-189. [DOI: 10.1016/j.tibtech.2016.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 11/25/2022]
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38
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Xi HD, Zheng H, Guo W, Gañán-Calvo AM, Ai Y, Tsao CW, Zhou J, Li W, Huang Y, Nguyen NT, Tan SH. Active droplet sorting in microfluidics: a review. LAB ON A CHIP 2017; 17:751-771. [PMID: 28197601 DOI: 10.1039/c6lc01435f] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ability to manipulate and sort droplets is a fundamental issue in droplet-based microfluidics. Various lab-on-a-chip applications can only be realized if droplets are systematically categorized and sorted. These micron-sized droplets act as ideal reactors which compartmentalize different biological and chemical reagents. Array processing of these droplets hinges on the competence of the sorting and integration into the fluidic system. Recent technological advances only allow droplets to be actively sorted at the rate of kilohertz or less. In this review, we present state-of-the-art technologies which are implemented to efficiently sort droplets. We classify the concepts according to the type of energy implemented into the system. We also discuss various key issues and provide insights into various systems.
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Affiliation(s)
- Heng-Dong Xi
- School of Aeronautics, Northwestern Polytechnical University, 127 West Youyi Rd., Xi'an, Shaanxi, China
| | - Hao Zheng
- School of Aeronautics, Northwestern Polytechnical University, 127 West Youyi Rd., Xi'an, Shaanxi, China
| | - Wei Guo
- School of Aeronautics, Northwestern Polytechnical University, 127 West Youyi Rd., Xi'an, Shaanxi, China and Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia.
| | - Alfonso M Gañán-Calvo
- Depto. de Ingeniería Aeroespacial y Mecánica de Fluidos, Universidad de Sevilla, E-41092 Sevilla, Spain
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore
| | - Chia-Wen Tsao
- Department of Mechanical Engineering, National Central University, No. 300, Zhongda Rd, Taoyuan, Taiwan
| | - Jun Zhou
- School of Information and Communication Technology, Griffith University, Nathan, QLD 4111, Australia
| | - Weihua Li
- School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yanyi Huang
- Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia.
| | - Say Hwa Tan
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia.
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39
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Molecular crowding improves bead-based padlock rolling circle amplification. Anal Biochem 2017; 519:15-18. [DOI: 10.1016/j.ab.2016.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 11/21/2022]
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40
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Digital Microfluidics Assisted Sealing of Individual Magnetic Particles in Femtoliter-Sized Reaction Wells for Single-Molecule Detection. Methods Mol Biol 2017. [PMID: 28044289 DOI: 10.1007/978-1-4939-6734-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Digital microfluidics has emerged in the last years as a promising liquid handling technology for a variety of applications. Here, we describe in detail how to build up an electrowetting-on-dielectric-based digital microfluidic chip with unique advantages for performing single-molecule detection. We illustrate how superparamagnetic particles can be printed with very high loading efficiency (over 98 %) and single-particle resolution in the microwell array patterned in the Teflon-AF® surface of the grounding plate of the chip. Finally, the potential of the device for its application to single-molecule detection is demonstrated by the ultrasensitive detection of the biotinylated enzyme β-Galactosidase captured on streptavidin-coated particles in the described platform.
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Abstract
The development of microfabricated devices that will provide high-throughput quantitative data and high resolution in a fast, repeatable and reproducible manner is essential for plant biology research.
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Affiliation(s)
- Meltem Elitaş
- Department of Mechatronics
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Meral Yüce
- Nanotechnology Research and Application Centre
- Sabanci University
- 34956, Istanbul
- Turkey
| | - Hikmet Budak
- Department of Molecular Biology
- Genetics and Bioengineering
- Faculty of Engineering and Natural Sciences
- Sabanci University
- 34956, Istanbul
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Seale B, Lam C, Rackus DG, Chamberlain MD, Liu C, Wheeler AR. Digital Microfluidics for Immunoprecipitation. Anal Chem 2016; 88:10223-10230. [PMID: 27700039 DOI: 10.1021/acs.analchem.6b02915] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Immunoprecipitation (IP) is a common method for isolating a targeted protein from a complex sample such as blood, serum, or cell lysate. In particular, IP is often used as the primary means of target purification for the analysis by mass spectrometry of novel biologically derived pharmaceuticals, with particular utility for the identification of molecules bound to a protein target. Unfortunately, IP is a labor-intensive technique, is difficult to perform in parallel, and has limited options for automation. Furthermore, the technique is typically limited to large sample volumes, making the application of IP cleanup to precious samples nearly impossible. In recognition of these challenges, we introduce a method for performing microscale IP using magnetic particles and digital microfluidics (DMF-IP). The new method allows for 80% recovery of model proteins from approximately microliter volumes of serum in a sample-to-answer run time of approximately 25 min. Uniquely, analytes are eluted from these small samples in a format compatible with direct analysis by mass spectrometry. To extend the technique to be useful for large samples, we also developed a macro-to-microscale interface called preconcentration using liquid intake by paper (P-CLIP). This technique allows for efficient analysis of samples >100× larger than are typically processed on microfluidic devices. As described herein, DMF-IP and P-CLIP-DMF-IP are rapid, automated, and multiplexed methods that have the potential to reduce the time and effort required for IP sample preparations with applications in the fields of pharmacy, biomarker discovery, and protein biology.
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Affiliation(s)
- Brendon Seale
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Charis Lam
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Darius G Rackus
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research , 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research , 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Chang Liu
- SCIEX , 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Donnelly Centre for Cellular and Biomolecular Research , 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario M5S 3G9, Canada
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Label-free detection of real-time DNA amplification using a nanofluidic diffraction grating. Sci Rep 2016; 6:31642. [PMID: 27531471 PMCID: PMC4987677 DOI: 10.1038/srep31642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/21/2016] [Indexed: 02/06/2023] Open
Abstract
Quantitative DNA amplification using fluorescence labeling has played an important role in the recent, rapid progress of basic medical and molecular biological research. Here we report a label-free detection of real-time DNA amplification using a nanofluidic diffraction grating. Our detection system observed intensity changes during DNA amplification of diffracted light derived from the passage of a laser beam through nanochannels embedded in a microchannel. Numerical simulations revealed that the diffracted light intensity change in the nanofluidic diffraction grating was attributed to the change of refractive index. We showed the first case reported to date for label-free detection of real-time DNA amplification, such as specific DNA sequences from tubercle bacilli (TB) and human papillomavirus (HPV). Since our developed system allows quantification of the initial concentration of amplified DNA molecules ranging from 1 fM to 1 pM, we expect that it will offer a new strategy for developing fundamental techniques of medical applications.
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Movafaghi S, Wang W, Metzger A, Williams DD, Williams JD, Kota AK. Tunable superomniphobic surfaces for sorting droplets by surface tension. LAB ON A CHIP 2016; 16:3204-9. [PMID: 27412084 DOI: 10.1039/c6lc00673f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We utilized tunable superomniphobic surfaces with flower-like TiO2 nanostructures to fabricate a simple device with precisely tailored surface energy domains that, for the first time, can sort droplets by surface tension. We envision that our methodology for droplet sorting will enable inexpensive and energy-efficient analytical devices for personalized point-of-care diagnostic platforms, lab-on-a-chip systems, biochemical assays and biosensors.
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Affiliation(s)
- S Movafaghi
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - W Wang
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - A Metzger
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - D D Williams
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - J D Williams
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - A K Kota
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523, USA. and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
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45
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Gooding JJ, Gaus K. Single‐Molecule Sensors: Challenges and Opportunities for Quantitative Analysis. Angew Chem Int Ed Engl 2016; 55:11354-66. [DOI: 10.1002/anie.201600495] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/17/2016] [Indexed: 11/09/2022]
Affiliation(s)
- J. Justin Gooding
- The University of New South Wales School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, UNSW Sydney 2052 Australia
| | - Katharina Gaus
- The University of New South Wales EMBL Australia Node in Single Molecule Science ARC Centre of Excellence in Advanced Molecular Imaging Sydney 2052 Australia
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Gooding JJ, Gaus K. Einzelmolekül‐Sensoren: Herausforderungen und Möglichkeiten für die quantitative Analyse. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- J. Justin Gooding
- The University of New South Wales School of Chemistry, Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, UNSW Sydney 2052 Australien
| | - Katharina Gaus
- The University of New South Wales EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging,UNSW Sydney 2052 Australien
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Production of dumbbell probe through hairpin cleavage-ligation and increasing RCA sensitivity and specificity by circle to circle amplification. Sci Rep 2016; 6:29229. [PMID: 27385060 PMCID: PMC4935871 DOI: 10.1038/srep29229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/16/2016] [Indexed: 11/23/2022] Open
Abstract
Dumbbell probe (DP) attracts increasing interests in rolling circle amplification (RCA). A universal DP production method through cleavage-ligation of hairpin was proposed and optimized. The production is characterized by restriction endonuclease (RE)-induced cleavage ends ligation. It has the advantage of phosphorylation-free, splint-free and purification-free. To optimize designing, we found that the position of RE cleavage sequence in the stem and the primer position in the loop affected the formation and amplification of DP obviously. Both sticky and blunt ends cleaved by RE produce DP efficiently. Moreover, we introduced this DP into circle to circle (C2C) RCA based on the same cleavage-ligation principle, and acquired high sensitivity. By combining a two-ligation design and the C2C strategy, specificity for detecting let-7 family members was increased extremely. Furthermore, coreaction of different steps facilitated convenient formation and amplification process of DP.
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Pérez-Ruiz E, Lammertyn J, Spasic D. Evaluation of different strategies for magnetic particle functionalization with DNA aptamers. N Biotechnol 2016; 33:755-762. [PMID: 27318011 DOI: 10.1016/j.nbt.2016.06.1459] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/13/2016] [Accepted: 06/13/2016] [Indexed: 11/30/2022]
Abstract
The optimal bio-functionalization of magnetic particles is essential for developing magnetic particle-based bioassays. Whereas functionalization with antibodies is generally well established, immobilization of DNA probes, such as aptamers, is not yet fully explored. In this work, four different types of commercially available magnetic particles, coated with streptavidin, maleimide or carboxyl groups, were evaluated for their surface coverage with aptamer bioreceptors, efficiency in capturing target protein and non-specific protein adsorption on their surface. A recently developed aptamer against the peanut allergen, Ara h 1 protein, was used as a model system. Conjugation of biotinylated Ara h 1 aptamer to the streptavidin particles led to the highest surface coverage, whereas the coverage of maleimide particles was 25% lower. Carboxylated particles appeared to be inadequate for DNA functionalization. Streptavidin particles also showed the greatest target capturing efficiency, comparable to the one of particles functionalized with anti-Ara h 1 antibody. The performance of streptavidin particles was additionally tested in a sandwich assay with the aptamer as a capture receptor on the particle surface. While the limit of detection obtained was comparable to the same assay system with antibody as capture receptor, it was superior to previously reported values using the same aptamer in similar assay schemes with different detection platforms. These results point to the promising application of the Ara h 1 aptamer-functionalized particles in bioassay development.
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Affiliation(s)
- Elena Pérez-Ruiz
- Department of Biosystems-MeBioS-Biosensor Group, KU Leuven, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems-MeBioS-Biosensor Group, KU Leuven, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems-MeBioS-Biosensor Group, KU Leuven, Leuven, Belgium
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Valiadi M, Kalsi S, Jones IGF, Turner C, Sutton JM, Morgan H. Simple and rapid sample preparation system for the molecular detection of antibiotic resistant pathogens in human urine. Biomed Microdevices 2016; 18:18. [PMID: 26846875 PMCID: PMC4742488 DOI: 10.1007/s10544-016-0031-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance in urinary tract infections (UTIs) can cause significant complications without quick detection and appropriate treatment. We describe a new approach to capture, concentrate and prepare amplification-ready DNA from antibiotic resistant bacteria in human urine samples. Klebsiella pneumoniae NCTC13443 (bla CTX-M-15 positive) spiked into filtered human urine was used as a model system. Bacteria were captured using anion exchange diaethylaminoethyl (DEAE) magnetic microparticles and concentrated 200-fold within ~3.5 min using a custom, valve-less microfluidic chip. Eight samples were processed in parallel, and DNA was released using heat lysis from an integrated resistive heater. The crude cell lysate was used for real time Recombinase Polymerase Amplification (RPA) of the bla CTX-M-15 gene. The end to end processing time was approximately 15 min with a limit of detection of 1000 bacteria in 1 mL urine.
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Affiliation(s)
- Martha Valiadi
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sumit Kalsi
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Isaac G F Jones
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Carrie Turner
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - J Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Hywel Morgan
- Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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Streptavidin-modified monodispersed magnetic poly(2-hydroxyethyl methacrylate) microspheres as solid support in DNA-based molecular protocols. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 61:362-7. [PMID: 26838862 DOI: 10.1016/j.msec.2015.12.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 10/12/2015] [Accepted: 12/28/2015] [Indexed: 01/16/2023]
Abstract
Molecular diagnostics may provide tailored and cost efficient treatment for infectious disease and cancer. Rolling circle amplification (RCA) of padlock probes guarantees high specificity to identify nucleic acid targets down to single nucleotide resolution in a multiplex fashion. This makes the assay suitable for molecular analysis of various diseases, and interesting to integrate into automated devices for point-of-care analysis. A critical prerequisite for many molecular assays is (i) target-specific isolation from complex clinical samples and (ii) removal of reagents, inhibitors and contaminants between reaction steps. Efficient solid supports are therefore essential to enable multi-step, multi-analyte protocols. Superparamagnetic micro- and nanoparticles, with large surface area and rapid liquid-phase kinetics, are attractive for multi-step protocols. Recently, streptavidin-modified magnetic monodispersed poly(2-hydroxyethyl methacrylate) (STV-mag.PHEMA) microspheres were developed by multiple swelling polymerization. They are easily separated by a magnet and exhibit low non-specific protein sorption. In this study, the performance and the binding efficiency of STV-mag.PHEMA was addressed by circle-to-circle amplification (C2CA). A lower number of RCA products were detected as compared to the gold standard Dynabeads. Nevertheless, this study was the first to successfully adapt STV-mag.PHEMA microspheres as solid support in a DNA-based protocol, which is an important finding. The STV-mag.PHEMA microspheres were larger with about 16 times less surface area as compared to the Dynabeads, which might partly explain the lower rolling circle product (RCP) count obtained. Further research is currently ongoing comparing particles of similar sizes and optimizing reaction conditions to establish their full utility in the field. Ultimately, low cost and versatile particles are a great resource to facilitate future clinical molecular diagnostics.
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