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Sytu MRC, Cho DH, Hahm JI. Self-Assembled Block Copolymers as a Facile Pathway to Create Functional Nanobiosensor and Nanobiomaterial Surfaces. Polymers (Basel) 2024; 16:1267. [PMID: 38732737 PMCID: PMC11085100 DOI: 10.3390/polym16091267] [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: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Block copolymer (BCP) surfaces permit an exquisite level of nanoscale control in biomolecular assemblies solely based on self-assembly. Owing to this, BCP-based biomolecular assembly represents a much-needed, new paradigm for creating nanobiosensors and nanobiomaterials without the need for costly and time-consuming fabrication steps. Research endeavors in the BCP nanobiotechnology field have led to stimulating results that can promote our current understanding of biomolecular interactions at a solid interface to the never-explored size regimes comparable to individual biomolecules. Encouraging research outcomes have also been reported for the stability and activity of biomolecules bound on BCP thin film surfaces. A wide range of single and multicomponent biomolecules and BCP systems has been assessed to substantiate the potential utility in practical applications as next-generation nanobiosensors, nanobiodevices, and biomaterials. To this end, this Review highlights pioneering research efforts made in the BCP nanobiotechnology area. The discussions will be focused on those works particularly pertaining to nanoscale surface assembly of functional biomolecules, biomolecular interaction properties unique to nanoscale polymer interfaces, functionality of nanoscale surface-bound biomolecules, and specific examples in biosensing. Systems involving the incorporation of biomolecules as one of the blocks in BCPs, i.e., DNA-BCP hybrids, protein-BCP conjugates, and isolated BCP micelles of bioligand carriers used in drug delivery, are outside of the scope of this Review. Looking ahead, there awaits plenty of exciting research opportunities to advance the research field of BCP nanobiotechnology by capitalizing on the fundamental groundwork laid so far for the biomolecular interactions on BCP surfaces. In order to better guide the path forward, key fundamental questions yet to be addressed by the field are identified. In addition, future research directions of BCP nanobiotechnology are contemplated in the concluding section of this Review.
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Affiliation(s)
- Marion Ryan C. Sytu
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
| | - David H. Cho
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA;
| | - Jong-in Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
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2
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Shigemori H, Fujita S, Tamiya E, Nagai H. Miniaturization of CRISPR/Cas12-Based DNA Sensor Array by Non-Contact Printing. MICROMACHINES 2024; 15:144. [PMID: 38258263 PMCID: PMC10818962 DOI: 10.3390/mi15010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
DNA microarrays have been applied for comprehensive genotyping, but remain a drawback in complicated operations. As a solution, we previously reported the solid-phase collateral cleavage (SPCC) system based on the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 12 (CRISPR/Cas12). Surface-immobilized Cas12-CRISPR RNA (crRNA) can directly hybridize target double-stranded DNA (dsDNA) and subsequently produce a signal via the cleavage of single-stranded DNA (ssDNA) reporter immobilized on the same spot. Therefore, SPCC-based multiplex dsDNA detection can be performed easily. This study reports the miniaturization of SPCC-based spots patterned by a non-contact printer and its performance in comprehensive genotyping on a massively accumulated array. Initially, printing, immobilization, and washing processes of Cas12-crRNA were established to fabricate the non-contact-patterned SPCC-based sensor array. A target dsDNA concentration response was obtained based on the developed sensor array, even with a spot diameter of 0.64 ± 0.05 mm. Also, the limit of detection was 572 pM, 531 pM, and 3.04 nM with 40, 20, and 10 nL-printing of Cas12-crRNA, respectively. Furthermore, the sensor array specifically detected three dsDNA sequences in one-pot multiplexing; therefore, the feasibility of comprehensive genotyping was confirmed. These results demonstrate that our technology can be miniaturized as a CRISPR/Cas12-based microarray by using non-contact printing. In the future, the non-contact-patterned SPCC-based sensor array can be applied as an alternative tool to DNA microarrays.
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Affiliation(s)
- Hiroki Shigemori
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-0011, Hyogo, Japan
| | - Satoshi Fujita
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
| | - Eiichi Tamiya
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Osaka, Japan
| | - Hidenori Nagai
- Advanced Photonics and Biosensing Open Innovation Laboratory (PhotoBIO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Photonics Center Osaka University, 2-1 Yamada-Oka, Suita 565-0871, Osaka, Japan; (H.S.); (S.F.); (E.T.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-0011, Hyogo, Japan
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Aggarwal RT, Lai L, Li H. Microarray fabrication techniques for multiplexed bioassay applications. Anal Biochem 2023; 683:115369. [PMID: 37914004 DOI: 10.1016/j.ab.2023.115369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.
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Affiliation(s)
| | - Leyun Lai
- School of Engineering, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Huiyan Li
- School of Engineering, University of Guelph, Guelph, Ontario, N1G2W1, Canada.
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Aparna GM, Tetala KKR. Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules 2023; 13:biom13040602. [PMID: 37189350 DOI: 10.3390/biom13040602] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018–2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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Chen H, Li X, Li D. Superhydrophilic–superhydrophobic patterned surfaces: From simplified fabrication to emerging applications. NANOTECHNOLOGY AND PRECISION ENGINEERING 2022. [DOI: 10.1063/10.0013222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Superhydrophilic–superhydrophobic patterned surfaces constitute a branch of surface chemistry involving the two extreme states of superhydrophilicity and superhydrophobicity combined on the same surface in precise patterns. Such surfaces have many advantages, including controllable wettability, enrichment ability, accessibility, and the ability to manipulate and pattern water droplets, and they offer new functionalities and possibilities for a wide variety of emerging applications, such as microarrays, biomedical assays, microfluidics, and environmental protection. This review presents the basic theory, simplified fabrication, and emerging applications of superhydrophilic–superhydrophobic patterned surfaces. First, the fundamental theories of wettability that explain the spreading of a droplet on a solid surface are described. Then, the fabrication methods for preparing superhydrophilic–superhydrophobic patterned surfaces are introduced, and the emerging applications of such surfaces that are currently being explored are highlighted. Finally, the remaining challenges of constructing such surfaces and future applications that would benefit from their use are discussed.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Xiaoping Li
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
| | - Dachao Li
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, China
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Normandeau F, Ng A, Beaugrand M, Juncker D. Spatial Bias in Antibody Microarrays May Be an Underappreciated Source of Variability. ACS Sens 2021; 6:1796-1806. [PMID: 33973474 DOI: 10.1021/acssensors.0c02613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibody microarrays enable multiplexed protein detection with minimal reagent consumption, but they continue to be plagued by lack of reproducibility. Chemically functionalized glass slides are used as substrates, yet antibody binding spatial inhomogeneity across the slide has not been analyzed in antibody microarrays. Here, we characterize spatial bias across five commercial slides patterned with nine overlapping dense arrays (by combining three buffers and three different antibodies), and we measure signal variation for both antibody immobilization and the assay signal, generating 270 heatmaps. Spatial bias varied across models, and the coefficient of variation ranged from 4.6 to 50%, which was unexpectedly large. Next, we evaluated three layouts of spot replicates-local, random, and structured random-for their capacity to predict assay variation. Local replicates are widely used but systematically underestimate the whole-slide variation by up to seven times; structured random replicates gave the most accurate estimation. Our results highlight the risk and consequences of using local replicates: the underappreciation of spatial bias as a source of variability, poor assay reproducibility, and possible overconfidence in assay results. We recommend the detailed characterization of spatial bias for antibody microarrays and the description and use of distributed positive replicates for research and clinical applications.
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Affiliation(s)
- Frédéric Normandeau
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Andy Ng
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Maiwenn Beaugrand
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - David Juncker
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
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Juárez MJ, Ibáñez-Echevarria E, de Rojas DHF, Maquieira Á, Morais S. Multiplexed analytical approaches to beta-lactam allergy in vitro testing standardization. Anal Chim Acta 2021; 1173:338656. [PMID: 34172156 DOI: 10.1016/j.aca.2021.338656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/05/2021] [Accepted: 05/15/2021] [Indexed: 11/29/2022]
Abstract
The suspicion of beta-lactam allergy directly contributes to the prescription of antibiotics that diverge from the guidelines, increasing antimicrobial resistance, one of the biggest threats to global health. In vitro quantification of specific IgE is very useful for monitoring allergy, as it confirms or rules out immediate beta-lactam drug allergy and helps find safe alternative antibiotic stewardship. However, reliable in vitro quantification of specific IgE to beta-lactam antibiotics by immunoassay is challenging because of the difficulty of having selective immunoreagents, mainly beta-lactam antigens, and its low concentration levels in serum. Thus, reliable and sensitive in vitro tests for multiplex detection of allergy to different beta-lactam antibiotics is currently essential for clinical diagnosis. Nevertheless, the lack of standardization of quantitative in vitro methods makes the comparison and interpretation of the results difficult. Here, as proof of concept, we report an improved multiplex microimmunoassay for beta-lactam allergy in vitro testing standardization. The results revealed that homologous calibration allows reliable quantification of specific IgE in human serum at very low concentrations (144 ng L-1). Moreover, the reproducibility of the results increases 2-fold using an internal standard, achieving accurate quantitative information: 93% and 106% recovery for penicillin and amoxicillin, respectively. We simultaneously evaluated the reliability of the improved multiplexed in vitro method in a cohort of 40 human serum samples and achieved excellent agreement (0.99) with a currently used in vitro test.
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Affiliation(s)
- María José Juárez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València-Universitat de València, Camino de Vera S/n, 46022, Valencia, Spain
| | - Ethel Ibáñez-Echevarria
- Hospital Universitari I Politènic La Fe, Servicio de Alergia, Avinguda de Fernando Abril Martorell, 106, 46026, València, Spain
| | | | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València-Universitat de València, Camino de Vera S/n, 46022, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Camino de Vera S/n, 46022, Valencia, Spain; Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Av. Fernando Abril Martorell, 46026, Valencia, Spain
| | - Sergi Morais
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València-Universitat de València, Camino de Vera S/n, 46022, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Camino de Vera S/n, 46022, Valencia, Spain; Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, IIS La Fe, Av. Fernando Abril Martorell, 46026, Valencia, Spain.
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8
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Antibody Printing Technologies. Methods Mol Biol 2020. [PMID: 33237416 DOI: 10.1007/978-1-0716-1064-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.
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Pereiro I, Cors JF, Pané S, Nelson BJ, Kaigala GV. Underpinning transport phenomena for the patterning of biomolecules. Chem Soc Rev 2019; 48:1236-1254. [PMID: 30671579 DOI: 10.1039/c8cs00852c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Surface-based assays are increasingly being used in biology and medicine, which in turn demand increasing quantitation and reproducibility. This translates into more stringent requirements on the patterning of biological entities on surfaces (also referred to as biopatterning). This tutorial focuses on mass transport in the context of existing and emerging biopatterning technologies. We here develop a step-by-step analysis of how analyte transport affects surface kinetics, and of the advantages and limitations this entails in major categories of patterning methods, including evaporating sessile droplets, laminar flows in microfluidics or electrochemistry. Understanding these concepts is key to obtaining the desired pattern uniformity, coverage, analyte usage or processing time, and equally applicable to surface assays. A representative technological review accompanies each section, highlighting the technical progress enabled by transport control in e.g. microcontact printing, inkjet printing, dip-pen nanolithography and microfluidic probes. We believe this tutorial will serve researchers to better understand available patterning methods/principles, optimize conditions and to help design protocols/assays. By highlighting fundamental challenges and available approaches, we wish to trigger the development of new surface patterning methods and assays.
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Affiliation(s)
- Iago Pereiro
- IBM Research - Zurich, Säumerstrasse 4, Rüschlikon, 8803, Switzerland.
| | - Julien F Cors
- IBM Research - Zurich, Säumerstrasse 4, Rüschlikon, 8803, Switzerland. and Institute of Robotics and Intelligent Systems, ETH Zurich, Zurich, 8092, Switzerland
| | - Salvador Pané
- Institute of Robotics and Intelligent Systems, ETH Zurich, Zurich, 8092, Switzerland
| | - Bradley J Nelson
- Institute of Robotics and Intelligent Systems, ETH Zurich, Zurich, 8092, Switzerland
| | - Govind V Kaigala
- IBM Research - Zurich, Säumerstrasse 4, Rüschlikon, 8803, Switzerland.
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