1
|
Li T, You R, Shen X, Li Z, Yang Y, Han Z, Duan X. Reconfigurable acoustic streaming tweezers enabled portable liquid handler for nucleic acid extraction. ULTRASONICS SONOCHEMISTRY 2025; 119:107404. [PMID: 40451113 PMCID: PMC12162031 DOI: 10.1016/j.ultsonch.2025.107404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 02/09/2025] [Accepted: 05/27/2025] [Indexed: 06/16/2025]
Abstract
The extraction and purification of nucleic acids (NA) play a crucial role in biomedicine, as high-purity and efficient extraction are essential prerequisites for accurate molecular diagnosis. Consequently, beads clumping and complex peripherals hinder the development of portable NA extraction apparatus. In this study, a novel reconfigurable acoustic streaming tweezer (RAST) is proposed. Two MEMS fabricated solid-mounted thin-film piezoelectric resonators (SMRs) are integrated into a compact reaction chamber. The high-frequency (>1 GHz) acoustic wave induces fast liquid flow and particle movement through the Stokes drag. By carefully designing the structure of the device and the operation program, the RAST can be switched between the chip-based centrifuge-type particle separation and the vortex-type solution mixing modes, enabling automated NA extraction without complex peripherals. Numerical simulations and micro particle image velocimetry (PIV) experiments are conducted to thoroughly investigate the particle manipulations and mixing conditions in the double SMR mode (D-SMR) and the single SMR mode (S-SMR). A portable liquid handler based on the RAST is designed and applied to NA extraction from different samples (buffers, serum, and whole blood). After optimization, the system achieves an 80 % NA recovery rate from rat whole blood. Combined with real-time quantitative PCR, the detection sensitivity for adenovirus (DNA) and COVID-19 (RNA) is as low as 102 IU/mL. When handling samples smaller than 200 μL, the sensitivity is more than 1.56 times higher than that of commercial automated liquid handling systems.
Collapse
Affiliation(s)
- Tiechuan Li
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
| | - Rui You
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
| | - Xiaotian Shen
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
| | - Zhiwei Li
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
| | - Yang Yang
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
| | - Ziyu Han
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China
| | - Xuexin Duan
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China.
| |
Collapse
|
2
|
Lee EY, Lee M, Kim MG, Bae CE, Kim SH, Shin Y. Acid-activated bentonite for solid-phase nucleic acid extraction from various pathogenic samples. Anal Chim Acta 2025; 1352:343928. [PMID: 40210284 DOI: 10.1016/j.aca.2025.343928] [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: 12/13/2024] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 04/12/2025]
Abstract
BACKGROUND Despite significant advancements in nucleic acid testing technologies, current nucleic acid extraction methods are often limited by inefficiency, complexity, and a lack of versatility. To overcome these challenges, we have developed an innovative solid-phase extraction (SPE) method employing sulfuric acid-activated bentonite (SAB) for extracting nucleic acids from various sample types. RESULTS Activation with sulfuric acid expands the surface area of bentonite by 2.2 times, thereby enhancing its adsorption capacity and surface modification efficiency. To further improve extraction efficiency, we modified SAB through amine-functionalization using 3-aminopropyl(diethoxy)methylsilane (APDMS), resulting in the creation of APDMS-modified SAB (ASAB). This modification facilitates efficient nucleic acid binding via reversible interactions mediated by a homobifunctional imidoester (HI) reagent. Our ASAB-based SPE system offers a streamlined, universal protocol for isolating DNA, RNA, and miRNA from diverse samples, including clinical bodily fluids and culture media, in under 30 min. Moreover, the system effectively enriches low concentrations of negatively charged pathogens (down to 20 CFU/reaction) from large-volume samples (up to 50 mL) through a 30-min pre-enrichment step utilizing the positively charged ASAB-HI complex. Comparative testing with pooled human urine and plasma samples revealed up to a 3.95-fold increase in DNA recovery compared to commercial SPE kits. Additionally, the system demonstrated up to a 6.3-fold improvement in the isolation of unstable viral RNA from clinical nasopharyngeal swabs, as well as critical microRNA biomarkers. SIGNIFICANCE The versatility and high efficiency of nucleic acid recovery with our ASAB-based SPE system indicate its potential to revolutionize traditional SPE methods, positioning it as a universal nucleic acid extraction platform for molecular biology research.
Collapse
Affiliation(s)
- Eun Yeong Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Minju Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chae Eun Bae
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| |
Collapse
|
3
|
Arockiam S, Nguyen VT, Knappenberger M, Anderson C, Hansen M, Murugan V, Christen JB, Anderson KS. Rapid on-chip nucleic acid extraction for point-of-care salivary diagnostics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2025. [PMID: 40336490 DOI: 10.1039/d4ay02201g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]
Abstract
Point-of-care technologies have become an essential tool in molecular diagnostics. Traditional laboratory-based nucleic acid extraction methods are laborious, costly, and hard to implement in point-of-care (POC) settings. POC nucleic acid extraction methods using silica membranes pose a significant technical challenge to simplify and efficiently extract RNA from biofluids such as saliva without degradation. Here, we have focused on addressing the POC nucleic acid (NA) extraction challenges by optimizing the RNase inactivation, viral lysis, NA binding conditions, and NA elution and adapting it to on-chip extraction. We have evaluated reducing agents, chaotropic salt (guanidine HCl), heat, proteinase K treatment, and elution buffer conditions. We have formulated POC-Pure, a cost-effective, efficient custom buffer-extraction method using silica to bind and release nucleic acids from salivary samples. To purify and concentrate NA, we have fabricated a microfluidic chip using xurographic and laser cutting techniques which incorporates a three-way valve actuator. We assessed the downstream application compatibility of the POC-Pure method using a POC-suitable loop-mediated isothermal amplification (LAMP). The simplified POC-Pure extraction method can purify and concentrate DNA and RNA with a lower limit of detection under 0.25 copies per μL and 0.5 copies per μL, respectively, using a 200 μL sample input. Thus, we have developed and demonstrated an on-chip nucleic acid extraction from saliva.
Collapse
Affiliation(s)
- Siril Arockiam
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Vi T Nguyen
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Mark Knappenberger
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Clifford Anderson
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Michael Hansen
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Vel Murugan
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Jennifer Blain Christen
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| | - Karen S Anderson
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, PO Box 876401.
| |
Collapse
|
4
|
Song Q, Gao H, Cheng L, Mitchell WL, Zhu M, Mao Y. Emerging Initiated Chemical Vapor Deposition Nanocoatings for Sustainable Food and Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:6442-6455. [PMID: 40062506 DOI: 10.1021/acs.jafc.5c01820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
Abstract
Initiated chemical vapor deposition (iCVD) has emerged as a versatile technique for developing functional nanocoatings that address critical food and agricultural challenges. This review highlights the unique capacities of iCVD nanocoatings, which enable precise engineering of surface properties, such as targeted cellular and molecular interactions, antimicrobial activity, and fouling resistance. In addition, the solvent-free nature of iCVD is particularly advantageous for coating sensitive materials and complex geometries commonly used across food and agriculture applications. This review provides an overview of iCVD's chemistry, deposition mechanisms, and ability to control nanocoating morphology and composition. Key applications discussed include iCVD nanocoatings for food quality monitoring, pathogen detection, antimicrobial food packaging, biomass extraction, and irrigation water purification. By summarizing recent advancements and identifying emerging trends, this review showcases the potential of iCVD as a powerful tool for developing sustainable, nanoenabled solutions in modern food and agriculture production.
Collapse
Affiliation(s)
- Qing Song
- Strait Institute of Flexible Electronics (SIFE, Future Technologies), Fujian Key Laboratory of Flexible Electronics, Fujian Normal University and Strait Laboratory of Flexible Electronics (SLoFE), Fuzhou 350117, China
| | - Haijun Gao
- Strait Institute of Flexible Electronics (SIFE, Future Technologies), Fujian Key Laboratory of Flexible Electronics, Fujian Normal University and Strait Laboratory of Flexible Electronics (SLoFE), Fuzhou 350117, China
| | - Lin Cheng
- Strait Institute of Flexible Electronics (SIFE, Future Technologies), Fujian Key Laboratory of Flexible Electronics, Fujian Normal University and Strait Laboratory of Flexible Electronics (SLoFE), Fuzhou 350117, China
| | - Whitney L Mitchell
- Division of Natural Sciences, Lyon College, Batesville, Arkansas 72501, United States
| | - Mengfan Zhu
- Division of Natural Sciences, Lyon College, Batesville, Arkansas 72501, United States
| | - Yu Mao
- Department of Biosystems Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| |
Collapse
|
5
|
Wang J, Butler JE, Ladd AJC. Microfluidic purification of genomic DNA. Proc Natl Acad Sci U S A 2025; 122:e2417757122. [PMID: 39847326 PMCID: PMC11789158 DOI: 10.1073/pnas.2417757122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 12/20/2024] [Indexed: 01/24/2025] Open
Abstract
We describe a microfluidic device to extract DNA from a cell lysate, without the need for centrifuges, magnetic beads, or gels. Instead, separation is driven by transverse migration of DNA, which occurs when a polyelectrolyte solution flowing through a microfluidic channel is subjected to an electric field. The coupling of the weak shearing with the axial electric field is highly selective for long, flexible, charged molecules, of which DNA is the sole example in a typical cell lysate. As a result of migration to the walls, DNA is held near the channel inlet by electrophoresis (there is no flow near the channel walls), while the remaining components are eluted by the much larger (at least 10-fold) convective flow. We have demonstrated the feasibility of the device by recovering up to 40 ng of purified DNA in less than 30 min from 10 μL of Escherichia coli lysate. Gel electrophoresis indicates minimal additional fragmentation during purification, up to the maximum length recorded by the gel (60 kbp). Electropherograms were also obtained for purified mammalian DNA, using a Femto Pulse system (fragment lengths up to 165 kbp). Extracted samples show strong amplification by PCR, while the original lysate does not. Mixtures of λ-DNA and BSA were used to determine the extent of the separation of DNA from a physiological concentration of proteins (30 mg/mL). The protein concentration in the extract (0.3 to 0.5 ng/µL) was reduced by five orders of magnitude from the initial mixture.
Collapse
Affiliation(s)
- Jiayi Wang
- Department of Chemical Engineering, University of Florida, Gainesville, FL32611
| | - Jason E. Butler
- Department of Chemical Engineering, University of Florida, Gainesville, FL32611
| | - Anthony J. C. Ladd
- Department of Chemical Engineering, University of Florida, Gainesville, FL32611
| |
Collapse
|
6
|
Wanitchanon T, Chewapreecha C, Uttamapinant C. Integrating Genomic Data with the Development of CRISPR-Based Point-of-Care-Testing for Bacterial Infections. CURRENT CLINICAL MICROBIOLOGY REPORTS 2024; 11:241-258. [PMID: 39525369 PMCID: PMC11541280 DOI: 10.1007/s40588-024-00236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2024] [Indexed: 11/16/2024]
Abstract
Purpose of Review Bacterial infections and antibiotic resistance contribute to global mortality. Despite many infections being preventable and treatable, the lack of reliable and accessible diagnostic tools exacerbates these issues. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based diagnostics has emerged as a promising solution. However, the development of CRISPR diagnostics has often occurred in isolation, with limited integration of genomic data to guide target selection. In this review, we explore the synergy between bacterial genomics and CRISPR-based point-of-care tests (POCT), highlighting how genomic insights can inform target selection and enhance diagnostic accuracy. Recent Findings We review recent advances in CRISPR-based technologies, focusing on the critical role of target sequence selection in improving the sensitivity of CRISPR-based diagnostics. Additionally, we examine the implementation of these technologies in resource-limited settings across Asia and Africa, presenting successful case studies that demonstrate their potential. Summary The integration of bacterial genomics with CRISPR technology offers significant promise for the development of effective point-of-care diagnostics.
Collapse
Affiliation(s)
- Thanyapat Wanitchanon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbe, Wellcome Sanger Institute, Hinxton, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| |
Collapse
|
7
|
Yang Y, Wang Z, Xie H, Hu Y, Liu H. A SAW-Based Programmable Controlled RNA Detecting Device: Rapid In Situ Cytolysis-RNA Capture-RNA Release-PCR in One Mini Chamber. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309744. [PMID: 38773709 PMCID: PMC11304306 DOI: 10.1002/advs.202309744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/19/2024] [Indexed: 05/24/2024]
Abstract
Viral RNA detection is crucial in preventing and treating early infectious diseases. Traditional methods of RNA detection require a large amount of equipment and technical personnel. In this study, proposed a programmable controlled surface acoustic wave (SAW)-based RNA detecting device has been proposed. The proposed device can perform the entire viral RNA detection process, including cell lysis by cell-microparticle collision through SAW-induced liquid whirling, RNA capture by SAW-suspended magnetic beads, RNA elution through SAW-induced high streaming force, and PCR thermal cycling through SAW-generated heat. The device has completed all RNA detection steps in one mini chamber, requiring only 489 µl reagents for RNA extraction, much smaller than the amount used in manual RNA extraction (2065 µl). The experimental results have shown that PCR results from the device are comparable to those achieved via commercial qPCR instrumental detection. This work has demonstrated the potential of SAW-based lab-on-a-chip devices for point-of-care testing and provided a novel approach for rapidly detecting infectious diseases.
Collapse
Affiliation(s)
- Yupeng Yang
- Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518000P. R. China
- University of JinanJinan250022P. R. China
| | - Zenan Wang
- Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518000P. R. China
| | - Hetao Xie
- University of JinanJinan250022P. R. China
| | - Ying Hu
- Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518000P. R. China
| | - Hong Liu
- University of JinanJinan250022P. R. China
| |
Collapse
|
8
|
Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
Collapse
Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| |
Collapse
|
9
|
Wang Z, Liu M, Lin H, Zhu G, Dong Z, Wu N, Fan Y, Xu G, Chang L, Wang Y. An Ion Concentration Polarization Microplatform for Efficient Enrichment and Analysis of ctDNA. ACS NANO 2024; 18:2872-2884. [PMID: 38236597 DOI: 10.1021/acsnano.3c07137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Strategies for rapid, effective nucleic acid processing hold tremendous significance to the clinical analysis of circulating tumor DNA (ctDNA), a family of important markers indicating tumorigenesis and metastasis. However, traditional techniques remain challenging to achieve efficient DNA enrichment, further bringing about complicated operation and limited detection sensitivity. Here, we developed an ion concentration polarization microplatform that enabled highly rapid, efficient enrichment and purification of ctDNA from a variety of clinical samples, including serum, urine, and feces. The platform demonstrated efficiently separating and enriching ctDNA within 30 s, with a 100-fold improvement over traditional methods. Integrating an on-chip isothermal amplification module, the platform further achieved 100-fold enhanced sensitivity in ctDNA detection, which significantly eliminated false-negative results in the serum or urine samples due to the low abundance of ctDNA. Such a simple-designed platform offers a user-friendly yet powerful diagnosis technique with a wide applicability, ranging from early tumor diagnosis to infection screening.
Collapse
Affiliation(s)
- Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Ming Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guiying Zhu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yubo Fan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Shanghai Sci-Tech InnoCenter for Infection & Immunity, Shanghai, 200000, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| |
Collapse
|
10
|
Kang M, Jeong E, Kim JY, Yun SA, Jang MA, Jang JH, Kim TY, Huh HJ, Lee NY. Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay. Sci Rep 2023; 13:20364. [PMID: 37990045 PMCID: PMC10663557 DOI: 10.1038/s41598-023-47645-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
In the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
Collapse
Affiliation(s)
- Minhee Kang
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Eunjung Jeong
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji-Yeon Kim
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Sun Ae Yun
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| |
Collapse
|
11
|
Jiang L, Lan X, Ren L, Jin Z, Shan X, Yang M, Chang L. Single-molecule RNA capture-assisted droplet digital loop-mediated isothermal amplification for ultrasensitive and rapid detection of infectious pathogens. MICROSYSTEMS & NANOENGINEERING 2023; 9:118. [PMID: 37767528 PMCID: PMC10519972 DOI: 10.1038/s41378-023-00576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/16/2023] [Indexed: 09/29/2023]
Abstract
To minimize and control the transmission of infectious diseases, a sensitive, accurate, rapid, and robust assay strategy for application on-site screening is critical. Here, we report single-molecule RNA capture-assisted digital RT-LAMP (SCADL) for point-of-care testing of infectious diseases. Target RNA was captured and enriched by specific capture probes and oligonucleotide probes conjugated to magnetic beads, replacing laborious RNA extraction. Droplet generation, amplification, and the recording of results are all integrated on a microfluidic chip. In assaying commercial standard samples, quantitative results precisely corresponded to the actual concentration of samples. This method provides a limit of detection of 10 copies mL-1 for the N gene within 1 h, greatly reducing the need for skilled personnel and precision instruments. The ultrasensitivity, specificity, portability, rapidity and user-friendliness make SCADL a competitive candidate for the on-site screening of infectious diseases.
Collapse
Affiliation(s)
- Liying Jiang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
- Academy for Quantum Science and Technology, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Xianghao Lan
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Linjiao Ren
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Zhiyuan Jin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191 Beijing, China
| | - Xuchen Shan
- School of Physics, Beihang University, 100191 Beijing, China
| | - Mingzhu Yang
- Beijing Research Institute of Mechanical Equipment, 100143 Beijing, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191 Beijing, China
| |
Collapse
|
12
|
Li Y, Liu S, Wang Y, Wang Y, Li S, He N, Deng Y, Chen Z. Research on a Magnetic Separation-Based Rapid Nucleic Acid Extraction System and Its Detection Applications. BIOSENSORS 2023; 13:903. [PMID: 37887096 PMCID: PMC10605191 DOI: 10.3390/bios13100903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023]
Abstract
Nucleic acid extraction represents the "first step" in molecular diagnostic experiments. The quality of this extraction serves as a fundamental prerequisite for ensuring the accuracy of nucleic acid detection. This article presents a comprehensive design scheme for a rapid automated nucleic acid extraction system based on magnetic separation. The design and implementation of the system are analyzed and investigated in-depth, focusing on the core methods, hardware control, and software control of the automated nucleic acid extraction system. Additionally, a study and evaluation were carried out concerning the nucleic acid extraction and detection aspects encompassed by the system. The results demonstrate that the temperature deviation in the lysis and elution fluids is approximately ±1 °C, the positioning accuracy of the system's movement is ±0.005 mm, the average magnetic bead recovery rate is 94.98%, and the average nucleic acid recovery rate is 91.83%. The developed automated system and manual methods are employed for sample extraction, enabling the isolation of highly pure nucleic acids from bacteria, blood, and animal tissues for RT-PCR detection. The instrument employs lysis temperatures ranging from 70-80 °C, elution temperature of 80 °C, and drying time of 5-10 min, with a total extraction time of less than 35 min for different sample types. Overall, the system yields high nucleic acid concentration and purity, exhibits stable instrument operation, good repeatability, high efficiency, and low cost. It meets the requirements of genetic-level research and is worthy of clinical promotion and usage.
Collapse
Affiliation(s)
- Yao Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| | - Sha Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| | - Yuanyuan Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
- State Key Laboratory of Digital Medical Engineering, School of Biological and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (Y.L.); (S.L.); (Y.W.); (Y.W.); (S.L.); (N.H.); (Y.D.)
| |
Collapse
|
13
|
Wu M, Huang Y, Huang Y, Wang H, Li M, Zhou Y, Zhao H, Lan Y, Wu Z, Jia C, Feng S, Zhao J. Droplet magnetic-controlled microfluidic chip integrated nucleic acid extraction and amplification for the detection of pathogens and tumor mutation sites. Anal Chim Acta 2023; 1271:341469. [PMID: 37328249 DOI: 10.1016/j.aca.2023.341469] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/18/2023]
Abstract
Traditional nucleic acid extraction and detection is based on open operation, which may cause cross-contamination and aerosol formation. This study developed a droplet magnetic-controlled microfluidic chip integrated nucleic acid extraction, purification and amplification. The reagent is sealed in oil to form a droplet, and the nucleic acid is extracted and purified by controlling the movement of the magnetic beads (MBs) through a permanent magnet, ensuring a closed environment. This chip can automatically extract nucleic acid from multiple samples within 20 min, and can be directly placed in the in situ amplification instrument for amplification without further transfer of nucleic acid, characterized by simple, fast, time-saving and labor-saving. The results showed that the chip was able to detect <10 copies/test SARS-CoV-2 RNA, and EGFR exon 21 L858R mutations were detected in H1975 cells as low as 4 cells. In addition, on the basis of the droplet magnetic-controlled microfluidic chip, we further developed a multi-target detection chip, which used MBs to divide the nucleic acid of the sample into three parts. And the macrolides resistance mutations A2063G and A2064G, and the P1 gene of mycoplasma pneumoniae (MP) were successfully detected in clinical samples by the multi-target detection chip, providing the possibility for future application in the detection of multiple pathogens.
Collapse
Affiliation(s)
- Man Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhang Huang
- Shanghai Normal University, Shanghai, 200030, China
| | - Yaru Huang
- Shanghai Normal University, Shanghai, 200030, China
| | - Hua Wang
- Renji Hospital Affiliated to Shanghai Jiao Tong University, 200127, China
| | - Min Li
- Renji Hospital Affiliated to Shanghai Jiao Tong University, 200127, China
| | - Yang Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuwei Lan
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
14
|
Xesfyngi Y, Georgoutsou-Spyridonos M, Tripathy A, Milionis A, Poulikakos D, Mastellos DC, Tserepi A. A High-Performance Antibacterial Nanostructured ZnO Microfluidic Device for Controlled Bacterial Lysis and DNA Release. Antibiotics (Basel) 2023; 12:1276. [PMID: 37627695 PMCID: PMC10451374 DOI: 10.3390/antibiotics12081276] [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: 06/15/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
In this work, the antibacterial properties of nanostructured zinc oxide (ZnO) surfaces are explored by incorporating them as walls in a simple-to-fabricate microchannel device. Bacterial cell lysis is demonstrated and quantified in such a device, which functions due to the action of its nanostructured ZnO surfaces in contact with the working fluid. To shed light on the mechanism responsible for lysis, E. coli bacteria were incubated in zinc and nanostructured ZnO substrates, as well as the here-investigated ZnO-based microfluidic devices. The unprecedented killing efficiency of E. coli in nanostructured ZnO microchannels, effective after a 15 min incubation, paves the way for the implementation of such microfluidic chips in the disinfection of bacteria-containing solutions. In addition, the DNA release was confirmed by off-chip PCR and UV absorption measurements. The results indicate that the present nanostructured ZnO-based microfluidic chip can, under light, achieve partial inactivation of the released bacterial DNA via reactive oxygen species-mediated oxidative damage. The present device concept can find broader applications in cases where the presence of DNA in a sample is not desirable. Furthermore, the present microchannel device enables, in the dark, efficient release of bacterial DNA for downstream genomic DNA analysis. The demonstrated potential of this antibacterial device for tailored dual functionality in light/dark conditions is the main novel contribution of the present work.
Collapse
Affiliation(s)
- Yvonni Xesfyngi
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research (NCSR) “Demokritos”, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Greece; (Y.X.); (M.G.-S.)
| | - Maria Georgoutsou-Spyridonos
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research (NCSR) “Demokritos”, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Greece; (Y.X.); (M.G.-S.)
| | - Abinash Tripathy
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland; (A.T.); (A.M.); (D.P.)
| | - Athanasios Milionis
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland; (A.T.); (A.M.); (D.P.)
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland; (A.T.); (A.M.); (D.P.)
| | - Dimitrios C. Mastellos
- Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research (NCSR) “Demokritos”, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Greece;
| | - Angeliki Tserepi
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research (NCSR) “Demokritos”, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Greece; (Y.X.); (M.G.-S.)
| |
Collapse
|
15
|
Wang Y, Wang C, Zhou Z, Si J, Li S, Zeng Y, Deng Y, Chen Z. Advances in Simple, Rapid, and Contamination-Free Instantaneous Nucleic Acid Devices for Pathogen Detection. BIOSENSORS 2023; 13:732. [PMID: 37504131 PMCID: PMC10377012 DOI: 10.3390/bios13070732] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
Pathogenic pathogens invade the human body through various pathways, causing damage to host cells, tissues, and their functions, ultimately leading to the development of diseases and posing a threat to human health. The rapid and accurate detection of pathogenic pathogens in humans is crucial and pressing. Nucleic acid detection offers advantages such as higher sensitivity, accuracy, and specificity compared to antibody and antigen detection methods. However, conventional nucleic acid testing is time-consuming, labor-intensive, and requires sophisticated equipment and specialized medical personnel. Therefore, this review focuses on advanced nucleic acid testing systems that aim to address the issues of testing time, portability, degree of automation, and cross-contamination. These systems include extraction-free rapid nucleic acid testing, fully automated extraction, amplification, and detection, as well as fully enclosed testing and commercial nucleic acid testing equipment. Additionally, the biochemical methods used for extraction, amplification, and detection in nucleic acid testing are briefly described. We hope that this review will inspire further research and the development of more suitable extraction-free reagents and fully automated testing devices for rapid, point-of-care diagnostics.
Collapse
Affiliation(s)
- Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Chengming Wang
- Department of Cardiovascular Medicine, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou 412000, China
| | - Zepeng Zhou
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jiajia Si
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yezhan Zeng
- School of Electrical and Information Engineering, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| |
Collapse
|
16
|
Huang Z, Lyon CJ, Wang J, Lu S, Hu TY. CRISPR Assays for Disease Diagnosis: Progress to and Barriers Remaining for Clinical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301697. [PMID: 37162202 PMCID: PMC10369298 DOI: 10.1002/advs.202301697] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Numerous groups have employed the special properties of CRISPR/Cas systems to develop platforms that have broad potential applications for sensitive and specific detection of nucleic acid (NA) targets. However, few of these approaches have progressed to commercial or clinical applications. This review summarizes the properties of known CRISPR/Cas systems and their applications, challenges associated with the development of such assays, and opportunities to improve their performance or address unmet assay needs using nano-/micro-technology platforms. These include rapid and efficient sample preparation, integrated single-tube, amplification-free, quantifiable, multiplex, and non-NA assays. Finally, this review discusses the current outlook for such assays, including remaining barriers for clinical or point-of-care applications and their commercial development.
Collapse
Affiliation(s)
- Zhen Huang
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Jin Wang
- Tolo Biotechnology Company Limited333 Guiping RoadShanghai200233China
| | - Shuihua Lu
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
| | - Tony Y. Hu
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| |
Collapse
|
17
|
Malpartida-Cardenas K, Baum J, Cunnington A, Georgiou P, Rodriguez-Manzano J. A dual paper-based nucleic acid extraction method from blood in under ten minutes for point-of-care diagnostics. Analyst 2023; 148:3036-3044. [PMID: 37265396 PMCID: PMC10291277 DOI: 10.1039/d3an00296a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023]
Abstract
Nucleic acid extraction (NAE) plays a crucial role for diagnostic testing procedures. For decades, dried blood spots (DBS) have been used for serology, drug monitoring, and molecular studies. However, extracting nucleic acids from DBS remains a significant challenge, especially when attempting to implement these applications to the point-of-care (POC). To address this issue, we have developed a paper-based NAE method using cellulose filter papers (DBSFP) that operates without the need for electricity (at room temperature). Our method allows for NAE in less than 7 min, and it involves grade 3 filter paper pre-treated with 8% (v/v) igepal surfactant, 1 min washing step with 1× PBS, and 5 min incubation at room temperature in 1× TE buffer. The performance of the methodology was assessed with loop-mediated isothermal amplification (LAMP), targeting the human reference gene beta-actin and the kelch 13 gene from P. falciparum. The developed method was evaluated against FTA cards and magnetic bead-based purification, using time-to-positive (min) for comparative analysis. Furthermore, we optimised our approach to take advantage of the dual functionality of the paper-based extraction, allowing for elution (eluted disk) as well as direct placement of the disk in the LAMP reaction (in situ disk). This flexibility extends to eukaryotic cells, bacterial cells, and viral particles. We successfully validated the method for RNA/DNA detection and demonstrated its compatibility with whole blood stored in anticoagulants. Additionally, we studied the compatibility of DBSFP with colorimetric and lateral flow detection, showcasing its potential for POC applications. Across various tested matrices, targets, and experimental conditions, our results were comparable to those obtained using gold standard methods, highlighting the versatility of our methodology. In summary, this manuscript presents a cost-effective solution for NAE from DBS, enabling molecular testing in virtually any POC setting. When combined with LAMP, our approach provides sample-to-result detection in under 35 minutes.
Collapse
Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK.
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Jake Baum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, UK
- School of Medical Sciences, University of New South Wales, Australia
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK.
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | | |
Collapse
|
18
|
Jena S, Gaur D, Dubey NC, Tripathi BP. Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases. Int J Biol Macromol 2023:125089. [PMID: 37245760 DOI: 10.1016/j.ijbiomac.2023.125089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.
Collapse
Affiliation(s)
- Saikrushna Jena
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Divya Gaur
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Nidhi C Dubey
- Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
| |
Collapse
|
19
|
Ran J, Wang X, Liu Y, Yin S, Li S, Zhang L. Microreactor-based micro/nanomaterials: fabrication, advances, and outlook. MATERIALS HORIZONS 2023. [PMID: 37139613 DOI: 10.1039/d3mh00329a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Micro/nanomaterials are widely used in optoelectronics, environmental materials, bioimaging, agricultural industries, and drug delivery owing to their marvelous features, such as quantum tunneling, size, surface and boundary, and Coulomb blockade effects. Recently, microreactor technology has opened up broad prospects for green and sustainable chemical synthesis as a powerful tool for process intensification and microscale manipulation. This review focuses on recent progress in the microreactor synthesis of micro/nanomaterials. First, the fabrication and design principles of existing microreactors for producing micro/nanomaterials are summarized and classified. Afterwards, typical examples are shown to demonstrate the fabrication of micro/nanomaterials, including metal nanoparticles, inorganic nonmetallic nanoparticles, organic nanoparticles, Janus particles, and MOFs. Finally, the future research prospects and key issues of microreactor-based micro/nanomaterials are discussed. In short, microreactors provide new ideas and methods for the synthesis of micro/nanomaterials, which have huge potential and inestimable possibilities in large-scale production and scientific research.
Collapse
Affiliation(s)
- Jianfeng Ran
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China.
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
- Key Laboratory of Unconventional Metallurgy, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Xuxu Wang
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China.
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
- Key Laboratory of Unconventional Metallurgy, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Yuanhong Liu
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China.
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
- Key Laboratory of Unconventional Metallurgy, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Shaohua Yin
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China.
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
- Key Laboratory of Unconventional Metallurgy, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Shiwei Li
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China.
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
- Key Laboratory of Unconventional Metallurgy, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| | - Libo Zhang
- Faculty of Metallurgical and Energy Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650093, China.
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization, Kunming University of Science and Technology, Kunming, Yunnan 650093, China
- Key Laboratory of Unconventional Metallurgy, Kunming University of Science and Technology, Kunming 650093, Yunnan, China
| |
Collapse
|
20
|
Gao D, Ma Z, Jiang Y. Recent advances in microfluidic devices for foodborne pathogens detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
21
|
Grint I, Crea F, Vasiliadou R. The Combination of Electrochemistry and Microfluidic Technology in Drug Metabolism Studies. ChemistryOpen 2022; 11:e202200100. [PMID: 36166688 PMCID: PMC9716038 DOI: 10.1002/open.202200100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/25/2022] [Indexed: 01/31/2023] Open
Abstract
Drugs are metabolized within the liver (pH 7.4) by phase I and phase II metabolism. During the process, reactive metabolites can be formed that react covalently with biomolecules and induce toxicity. Identifying and detecting reactive metabolites is an important part of drug development. Preclinical and clinical investigations are conducted to assess the toxicity and safety of a new drug candidate. Electrochemistry coupled to mass spectrometry is an ideal complementary technique to the current preclinical studies, a pure instrumental approach without any purification steps and tedious protocols. The combination of microfluidics with electrochemistry towards the mimicry of drug metabolism offers portability, low volume of reagents and faster reaction times. This review explores the development of microfluidic electrochemical cells for mimicking drug metabolism.
Collapse
Affiliation(s)
- Isobel Grint
- School of Life, Health and Chemical SciencesThe Open UniversityWalton Hall, Karen HillsMilton KeynesMK7 6AAUK
| | - Francesco Crea
- School of Life, Health and Chemical SciencesThe Open UniversityWalton Hall, Karen HillsMilton KeynesMK7 6AAUK
| | - Rafaela Vasiliadou
- School of Life, Health and Chemical SciencesThe Open UniversityWalton Hall, Karen HillsMilton KeynesMK7 6AAUK
| |
Collapse
|
22
|
Current Trends and Challenges in Point-of-care Urinalysis of Biomarkers in Trace Amounts. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
23
|
A novel method for inward fluid displacement in centrifugal microdevices for highly integrated nucleic acid processing with long-term reagent storage. Anal Chim Acta 2022; 1221:340063. [DOI: 10.1016/j.aca.2022.340063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/20/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022]
|
24
|
Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
Collapse
Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
25
|
Choe SW, Kim B, Kim M. Progress of Microfluidic Continuous Separation Techniques for Micro-/Nanoscale Bioparticles. BIOSENSORS 2021; 11:464. [PMID: 34821680 PMCID: PMC8615634 DOI: 10.3390/bios11110464] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/07/2021] [Accepted: 11/12/2021] [Indexed: 05/03/2023]
Abstract
Separation of micro- and nano-sized biological particles, such as cells, proteins, and nucleotides, is at the heart of most biochemical sensing/analysis, including in vitro biosensing, diagnostics, drug development, proteomics, and genomics. However, most of the conventional particle separation techniques are based on membrane filtration techniques, whose efficiency is limited by membrane characteristics, such as pore size, porosity, surface charge density, or biocompatibility, which results in a reduction in the separation efficiency of bioparticles of various sizes and types. In addition, since other conventional separation methods, such as centrifugation, chromatography, and precipitation, are difficult to perform in a continuous manner, requiring multiple preparation steps with a relatively large minimum sample volume is necessary for stable bioprocessing. Recently, microfluidic engineering enables more efficient separation in a continuous flow with rapid processing of small volumes of rare biological samples, such as DNA, proteins, viruses, exosomes, and even cells. In this paper, we present a comprehensive review of the recent advances in microfluidic separation of micro-/nano-sized bioparticles by summarizing the physical principles behind the separation system and practical examples of biomedical applications.
Collapse
Affiliation(s)
- Se-woon Choe
- Department of Medical IT Convergence Engineering, Kumoh National Institute of Technology, Gumi 39253, Korea;
- Department of IT Convergence Engineering, Kumoh National Institute of Technology, Gumi 39253, Korea
| | - Bumjoo Kim
- Department of Mechanical Engineering and Automotive Engineering, Kongju National University, Cheonan 1223-24, Korea;
- Department of Future Convergence Engineering, Kongju National University, Cheonan 1223-24, Korea
| | - Minseok Kim
- Department of Mechanical System Engineering, Kumoh National Institute of Technology, Gumi 39177, Korea
- Department of Aeronautics, Mechanical and Electronic Convergence Engineering, Kumoh National Institute of Technology, Gumi 39177, Korea
| |
Collapse
|
26
|
He Y, Huang Q, He Y, Ji H, Zhang T, Wang B, Huang Z. A Low Excitation Working Frequency Capacitively Coupled Contactless Conductivity Detection (C 4D) Sensor for Microfluidic Devices. SENSORS 2021; 21:s21196381. [PMID: 34640701 PMCID: PMC8512373 DOI: 10.3390/s21196381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022]
Abstract
In this work, a new capacitively coupled contactless conductivity detection (C4D) sensor for microfluidic devices is developed. By introducing an LC circuit, the working frequency of the new C4D sensor can be lowered by the adjustments of the inductor and the capacitance of the LC circuit. The limits of detection (LODs) of the new C4D sensor for conductivity/ion concentration measurement can be improved. Conductivity measurement experiments with KCl solutions were carried out in microfluidic devices (500 µm × 50 µm). The experimental results indicate that the developed C4D sensor can realize the conductivity measurement with low working frequency (less than 50 kHz). The LOD of the C4D sensor for conductivity measurement is estimated to be 2.2 µS/cm. Furthermore, to show the effectiveness of the new C4D sensor for the concentration measurement of other ions (solutions), SO42− and Li+ ion concentration measurement experiments were also carried out at a working frequency of 29.70 kHz. The experimental results show that at low concentrations, the input-output characteristics of the C4D sensor for SO42− and Li+ ion concentration measurement show good linearity with the LODs estimated to be 8.2 µM and 19.0 µM, respectively.
Collapse
Affiliation(s)
| | | | | | - Haifeng Ji
- Correspondence: ; Tel.: +86-571-8795-2145
| | | | | | | |
Collapse
|