1
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Chen CA, Ho NYJ, Hsiao HY, Lin SS, Lai PL, Tsai TT. Smartphone-assisted fluorescence-based detection of sunrise-type smart amplification process and a 3D-printed ultraviolet light-emitting diode device for the diagnosis of tuberculosis. Biosens Bioelectron 2024; 244:115799. [PMID: 37918047 DOI: 10.1016/j.bios.2023.115799] [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: 09/19/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Accurate and rapid diagnosis of infectious diseases plays a key role in clinical practice, especially in resource-limited countries. In this study, we integrated sunrise-type smart amplification process (s-SmartAmp), a convenient and sensitive isothermal amplification method for nucleic acid, into a portable 3D-printed device equipped with smartphone-assisted image analysis capabilities to develop a novel fluorescence-based sensing system for the on-site diagnosis of tuberculosis (TB). To increase the efficiency of fluorescence (or Förster) resonance energy transfer, two types of sunrise probe systems were compared to detect the IS6110 DNA sequence of TB. Subsequently, linear regression was conducted to compare the performance of s-SmartAmp and loop-mediated isothermal amplification (LAMP). The results indicated that, compared with LAMP, s-SmartAmp yielded more stable and precise results with lower background interference and high linear correlation coefficients (R2 = 0.9994 and 1, respectively) for the FAM-TAMRA and FITC-BHQ-1 probe system. The detection time was 45 min with a detection limit of 10 fg/μL. To evaluate the performance of our proposed on-site sensing system, we used s-SmartAmp 3D-printed ultraviolet light-emitting diode device to test multiple clinical samples of TB. Our findings suggest that the proposed system has the potential to achieve accurate and rapid on-site diagnosis of TB.
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Affiliation(s)
- Chung-An Chen
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hui-Yi Hsiao
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Song-Shu Lin
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Po-Liang Lai
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University, Taoyuan, Taiwan.
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2
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Zhang X, Peng Y, Yao L, Shang H, Zheng Z, Chen W, Xu J. Self-Assembly of Multivalent Aptamer-Tethered DNA Monolayers Dedicated to a Fluorescence Polarization-Responsive Circular Isothermal Strand Displacement Amplification for Salmonella Assay. Anal Chem 2023; 95:2570-2578. [PMID: 36653941 DOI: 10.1021/acs.analchem.2c05448] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Pathogenic bacteria are pathogens widely spread that are capable of causing mild to life-threatening diseases in human beings or other organisms. Rationally organizing the simple helical motif of double-stranded DNA (dsDNA) tiles into designed ensemble structures with architecturally defined collective properties could lead to promising biosensing applications for pathogen detection. In this work, we facilely engineered multivalent hairpin aptamer probe-tethered DNA monolayers (MHAP-DNA monolayers) and applied them to build a fluorescence polarization-responsive circular isothermal strand displacement amplification (FP-CSDA) for Salmonella assay. In this system, the MHAP-DNA monolayers were constructed based on a dsDNA tile-directed self-assembly. A FAM-labeled reporting probe (RPFAM) with an inherent low FP signal serves as the signaling unit. The presence of target Salmonella leads to the trapping of F RPFAM into the super DNA monolayers via a target-triggered CSDA to peel off the tethered hairpin-structured aptamer probes (HAPs) responsible for the binding of RPFAM. As a result, the FP signal of the FAM fluorophore can be remarkably amplified due to the recycling of target Salmonella and the capacity of structural DNA materials to strongly restrict the free rotation of the FAM fluorophore but without a fluorescence quenching effect. Experimental results demonstrate that the FP assay is able to detect Salmonella with a low limit of detection (LOD) of 7.2 × 100 CFU/mL and high specificity. As a proof-of-concept study, we envision our study using DNA nanoarchitecture as the foundation to modulate CSDA-based FP assays, promising to open up a new avenue for disease diagnosis, food safety detection, and biochemical studies.
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Affiliation(s)
- Xinlei Zhang
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yubo Peng
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Li Yao
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Huijie Shang
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhi Zheng
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China
| | - Wei Chen
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jianguo Xu
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China
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3
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Cai G, Yang J, Wang L, Chen C, Cai C, Gong H. A point-to-point "cap" strategy to construct a highly selective dual-function molecularly-imprinted sensor for the simultaneous detection of HAV and HBV. Biosens Bioelectron 2023; 219:114794. [PMID: 36279822 DOI: 10.1016/j.bios.2022.114794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/02/2022] [Accepted: 10/07/2022] [Indexed: 11/19/2022]
Abstract
As an artificial biomimetic receptor, molecularly-imprinted polymer (MIP) has been widely used for the separation, enrichment and detection of various substances. However, due to the complexity of virus structure, huge volume and the existence of highly similar viruses, MIP shows unsatisfactory selectivity in virus detection. To overcome these issues, two kinds of virus nanoMIPs, just like a "cap", were synthesized by a solid-phase imprinting nanogel technique. The "cap" had no inner core and was much smaller than that of a conventional MIP, which was more favorable for mass transfer. Moreover, each "cap" could only combine with one target virus, which avoided the interference between large-volume virus molecules effectively. The two synthesized "caps" were mixed to construct a bifunctional MIP virus sensor for the simultaneous detection of Hepatitis A virus (HAV) and Hepatitis B virus (HBV). As expected, the selectivity factor (SF) for HBV detection reached 13.7, which was much higher than the reported virus MIP sensors (SF: 3-6), which was comparable to that of small molecular imprinting sensors. In addition, the high sensitivity toward HBV was 34.3 fM, and that of HAV was 27.1 pM. This method provides an idea for preparing high-selectivity biomacro-MIPs, as well as a method for the simultaneous detection of similar viruses with high sensitivity and selectivity. The recovery experiment of spiked serum showed that this method also has great practical application prospects.
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Affiliation(s)
- Ganping Cai
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Junyu Yang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Lingyun Wang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China; School of Materials Science and Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Chunyan Chen
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Changqun Cai
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
| | - Hang Gong
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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4
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Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9125242. [DOI: 10.1155/2022/9125242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/27/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder. Randomly selected transcriptome sequencing analysis confirmed the SPP1 gene is closely related to ESCC. It was found that the expression trend of SPP1 obtained by RPS18 and PPIA as internal reference genes were the same as that of sequencing. The results show that RPS18 and PPIA are stable reference genes, and PPIA + RPS18 are a suitable reference gene combination. This is a reference gene report that combines transcriptome sequencing analysis and only focuses on ESCC, which makes the quantification more precise, systematic, and standardized, and promotes gene regulation research and the early diagnosis of ESCC in the future.
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5
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Rapid heavy metal sensing platform: A case of triple signal amplification strategy for the sensitive detection of serum copper. Anal Chim Acta 2021; 1181:338908. [PMID: 34556231 DOI: 10.1016/j.aca.2021.338908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Heavy metals are considered as hazardous substances to human because of their toxicity, persistence and bioaccumulation, and the level in serum is an important factor to evaluate the caused health risk, which depends on efficient and sensitive analytical methods. Here, a triple signal-amplified electrochemical sensing platform based on metal-dependent DNAzymes was fabricated for sensitive determination of heavy metals in serum (copper as a model target). Under the optimized conditions, the proposed method showed good sensitivity (limit of detection, 0.33 fM for Cu2+) with excellent selectivity and stability, which is ascribed to: (i) tetrahedral DNA nanostructures (TDNs) that was used as a promising scaffold to adjust the selective transformation between heterogeneous and homogeneous reactions, preventing the nonspecific binding of electrodes surface and DNA probes; (ii) the magnetic beads (MBs) used which led to signal amplification and decreased background owing to its excellent properties of extracting equivalent targets from the complex samples; (iii) two signal amplification strategy of catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR). In addition, the proposed sensing platform displayed satisfactory accuracy through the validation with inductively coupled plasma-mass spectrometry (ICP-MS) and a spike-recovery analysis (recoveries, 87.92-111.61%; RSD, 4.89-8.85%), indicating the great potential for rapid and sensitive detection of Cu2+ or other metal ions.
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6
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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7
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Pumford EA, Lu J, Spaczai I, Prasetyo ME, Zheng EM, Zhang H, Kamei DT. Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics. Biosens Bioelectron 2020; 170:112674. [PMID: 33035900 PMCID: PMC7529604 DOI: 10.1016/j.bios.2020.112674] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023]
Abstract
Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.
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Affiliation(s)
- Elizabeth A Pumford
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Jiakun Lu
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Iza Spaczai
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Matthew E Prasetyo
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Elaine M Zheng
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Hanxu Zhang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Daniel T Kamei
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA.
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8
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Teng F, Wu X, Hong T, Munk GB, Libera M. Integrating nucleic acid sequence-based amplification and microlensing for high-sensitivity self-reporting detection. Analyst 2020; 145:7528-7533. [PMID: 32966360 DOI: 10.1039/d0an01231a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We use electron-beam patterned functional microgels to integrate self-reporting molecular beacons, dielectric microlenses, and solid-phase and/or solution-phase nucleic acid amplification in a viral-detection microarray model. The detection limits for different combinations of these elements range from 10-10 M for direct target-beacon hybridization alone to 10-18 M when all elements are integrated simultaneously.
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Affiliation(s)
- Feiyue Teng
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, New Jersey 07030, USA.
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9
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Rajendran VK, Bakthavathsalam P, Bergquist PL, Sunna A. Smartphone technology facilitates point-of-care nucleic acid diagnosis: a beginner's guide. Crit Rev Clin Lab Sci 2020; 58:77-100. [PMID: 32609551 DOI: 10.1080/10408363.2020.1781779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The reliable detection of nucleic acids at low concentrations in clinical samples like blood, urine and saliva, and in food can be achieved by nucleic acid amplification methods. Several portable and hand-held devices have been developed to translate these laboratory-based methods to point-of-care (POC) settings. POC diagnostic devices could potentially play an important role in environmental monitoring, health, and food safety. Use of a smartphone for nucleic acid testing has shown promising progress in endpoint as well as real-time analysis of various disease conditions. The emergence of smartphone-based POC devices together with paper-based sensors, microfluidic chips and digital droplet assays are used currently in many situations to provide quantitative detection of nucleic acid targets. State-of-the-art portable devices are commercially available and rapidly emerging smartphone-based POC devices that allow the performance of laboratory-quality colorimetric, fluorescent and electrochemical detection are described in this review. We present a comprehensive review of smartphone-based POC sensing applications, specifically on microbial diagnostics, assess their performance and propose recommendations for the future.
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Affiliation(s)
| | - Padmavathy Bakthavathsalam
- School of Chemistry and Australian Centre for Nanomedicine, University of New South Wales, Sydney, Australia
| | - Peter L Bergquist
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Department of Molecular Medicine & Pathology, University of Auckland, Auckland, New Zealand.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
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10
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Cross-priming isothermal amplification combined with nucleic acid test strips for detection of meat species. Anal Biochem 2020; 597:113672. [DOI: 10.1016/j.ab.2020.113672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/17/2022]
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11
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Tang Z, Choi G, Nouri R, Guan W. Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing. NANO LETTERS 2019; 19:7927-7934. [PMID: 31657939 DOI: 10.1021/acs.nanolett.9b03040] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Gihoon Choi
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Reza Nouri
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Weihua Guan
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biomedical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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12
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Hu J, Huang R, Sun Y, Wei X, Wang Y, Jiang C, Geng Y, Sun X, Jing J, Gao H, Wang Z, Dong C. Sensitive and rapid visual detection of Salmonella Typhimurium in milk based on recombinase polymerase amplification with lateral flow dipsticks. J Microbiol Methods 2019; 158:25-32. [DOI: 10.1016/j.mimet.2019.01.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022]
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13
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Kikuchi N, Reed A, Gerasimova YV, Kolpashchikov DM. Split Dapoxyl Aptamer for Sequence-Selective Analysis of Nucleic Acid Sequence Based Amplification Amplicons. Anal Chem 2019; 91:2667-2671. [PMID: 30680988 DOI: 10.1021/acs.analchem.8b03964] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hybridization probes have been used for the detection of single nucleotide variations (SNV) in DNA and RNA sequences in the mix-and-read formats. Among the most conventional are Taqman probes, which require expensive quantitative polymerase chain reaction (qPCR) instruments with melting capabilities. More affordable isothermal amplification format requires hybridization probes that can selectively detect SNVs isothermally. Here we designed a split DNA aptamer (SDA) hybridization probe based on a recently reported DNA sequence that binds a dapoxyl dye and increases its fluorescence ( Kato, T.; Shimada, I.; Kimura, R.; Hyuga, M., Light-up fluorophore-DNA aptamer pair for label-free turn-on aptamer sensors. Chem. Commun. 2016 , 52 , 4041 - 4044 ). SDA uses two DNA strands that have low affinity to the dapoxyl dye unless hybridized to abutting positions at a specific analyte and form a dye-binding site, which is accompanied by up to a 120-fold increase in fluorescence. SDA differentiates SNV in the inhA gene of Mycobacterium tuberculosis at ambient temperatures and detects a conserved region of the Zika virus after isothermal nucleic acid sequence based amplification (NASBA) reaction. The approach reported here can be used for detection of isothermal amplification products in the mix-and-read format as an alternative to qPCR.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Adam Reed
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Yulia V Gerasimova
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States
| | - Dmitry M Kolpashchikov
- Chemistry Department , University of Central Florida , 4111 Libra Drive , Orlando , 32816 , Florida United States.,Burnett School of Biomedical Sciences , University of Central Florida , Orlando , 32816 , Florida United States
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14
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Teng F, Libera M. Microlens Enhancement of Surface-Tethered Molecular Beacons. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14969-14974. [PMID: 30277788 DOI: 10.1021/acs.langmuir.8b02204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The tethering of molecular beacon oligonucleotide detection probes to surface-patterned poly(ethylene glycol) (PEG) microgels has enabled the integration of molecular beacons into a microarray format. The microgels not only localize the probes to specific surface positions but also maintain them in a waterlike environment. Here we extend the concept of microgel tethering to include dielectric microlenses. We show that streptavidin-functionalized polystyrene microspheres (3 μm diameter) can be colocalized with molecular beacons using biotinylated PEG gels in patterns ranging from pseudocontinuous microgel pads with lateral dimensions on the order of tens of micrometers to individual microgels with lateral dimensions on the order of 400-500 nm. We use a simplex assay based on Influenza A detection to study the lensing behavior. The microspheres increase the effective numerical aperture of the collection optics, and we find that a tethered microsphere increases the peak intensity collected from hybridized beacons between 1.5 and 10 times depending on the specific pattern size and areal density of microgels. The highest signal increase occurs when a single microsphere is tethered to a single isolated microgel. The tethering is highly self-directed and occurs in the individual-microgel case only when the microgel is close to the optic axis of the microsphere. This alignment minimizes spherical aberration and maximizes coupling of emitted fluorescent intensity into the collection optics.
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Affiliation(s)
- Feiyue Teng
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Matthew Libera
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
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