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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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Song J, Song Y, Jang H, Moon J, Kang H, Huh YM, Son HY, Rho HW, Park M, Lim EK, Jung J, Jung Y, Park HG, Lee KG, Im SG, Kang T. Elution-free DNA detection using CRISPR/Cas9-mediated light-up aptamer transcription: Toward all-in-one DNA purification and detection tube. Biosens Bioelectron 2023; 225:115085. [PMID: 36696850 DOI: 10.1016/j.bios.2023.115085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/31/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
Accurate and efficient detection of DNA is crucial for disease diagnosis and health monitoring. The traditional methods for DNA analysis involve multiple steps, including sample preparation, lysis, extraction, amplification, and detection. In this study, we present a one-step elution-free DNA analysis method based on the combination of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated light-up aptamer transcription (CLAT) assay and a DNA-capturing poly(2-dimethylaminomethyl styrene) (pDMAMS)-coated tube. The sample solution and lysis buffer are added to the pDMAMS-coated tube, and the DNA is efficiently captured on the surface via electrostatic interaction and directly detected by CLAT assay. The ability of the CRISPR/Cas9 system to specifically recognize DNA enables direct detection of DNA captured on the pDMAMS-coated tube. The combination of CLAT assay and pDMAMS-coated tube simplifies DNA detection in a single tube without the need for complicated extraction steps, improving sensitivity. Our platform demonstrated attomolar sensitivity in the detection of target DNA in cell lysate (0.92 aM), urine (7.7 aM), and plasma (94.6 aM) samples within 1 h. The practical applicability of this method was further demonstrated in experiments with tumor-bearing mice. We believe that this approach brings us closer to an all-in-one DNA purification and detection tube system and has potential applications in tissue and liquid biopsies, as well as various other DNA sensing applications.
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Affiliation(s)
- Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Younseong Song
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jeong Moon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyunju Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Department of Biochemistry & Molecular Biology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Severance Biomedical Science Institute, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; YUHS-KRIBB Medical Convergence Research Institute, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Severance Biomedical Science Institute, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyun Wook Rho
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Mirae Park
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Yongwon Jung
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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Ezenarro JJ, Mas J, Muñoz-Berbel X, Uria N. Advances in bacterial concentration methods and their integration in portable detection platforms: A review. Anal Chim Acta 2022; 1209:339079. [PMID: 35569858 DOI: 10.1016/j.aca.2021.339079] [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: 05/14/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022]
Abstract
Early detection and identification of microbial contaminants is crucial in many sectors, including clinical diagnostics, food quality control and environmental monitoring. Biosensors have recently gained attention among other bacterial detection technologies due to their simplicity, rapid response, selectivity, and integration/miniaturization potential in portable microfluidic platforms. However, biosensors are limited to the analysis of small sample volumes, and pre-concentration steps are necessary to reach the low sensitivity levels of few bacteria per mL required in the analysis of real clinical, industrial or environmental samples. Many platforms already exist where bacterial detection and separation/accumulation systems are integrated in a single platform, but they have not been compiled and critically analysed. This review reports on most recent advances in bacterial concentration/detection platforms with emphasis on the concentration strategy. Systems based on five concentration strategies, i.e. centrifugation, filtration, magnetic separation, electric separation or acoustophoresis, are here presented and compared in terms of processed sample volume, concentration efficiency, concentration time, ability to work with different types of samples, and integration potential, among others. The critical evaluation presented in the review is envision to facilitate the development of future platforms for fast, sensitive and in situ bacterial detection in real sample.
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Affiliation(s)
- Josune J Ezenarro
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola Del Vallès, Spain; Waterologies S.L, C/ Dinamarca, 3 (nave 9), Polígono Industrial Les Comes, 08700, Igualada, Spain; Institut de Microelectrònica de Barcelona, IMB-CNM-CSIC, Campus UAB, 08193, Bellaterra, Spain.
| | - Jordi Mas
- Departament de Genètica I de Microbiologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola Del Vallès, Spain
| | - Xavier Muñoz-Berbel
- Institut de Microelectrònica de Barcelona, IMB-CNM-CSIC, Campus UAB, 08193, Bellaterra, Spain
| | - Naroa Uria
- Institut de Microelectrònica de Barcelona, IMB-CNM-CSIC, Campus UAB, 08193, Bellaterra, Spain; Arkyne Tehcnologies S.L (Bioo), Carrer de La Tecnologia, 17, 08840, Viladecans, Spain.
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Ren S, Zhang X, Li Z, Jian X, Zhao J, Song YY. Development of a pulse-induced electrochemical biosensor based on gluconamide for Gram-negative bacteria detection. Mikrochim Acta 2021; 188:399. [PMID: 34716816 DOI: 10.1007/s00604-021-05073-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022]
Abstract
Pathogenic bacteria can cause the outbreaks of disease and threaten human health, which stimulates the development of advanced detection techniques. Herein, a specific and sensitive electrochemical biosensor for Gram-negative bacteria was established based on the conductive polymer with artificial muscle properties. The effective recognition was achieved through the specific carbohydrate-carbohydrate interaction between gluconamide and lipopolysaccharide. The application of impulse voltage enhances the efficiency of recognition and shortens the detection time through the temporary deformation of the electrode surface, with a limit of detection (LOD) of 1 × 100 CFU/mL and a linear range of 1 × 100 - 1 × 106 CFU/mL for Escherichia coli (E. coli). In addition to the merits of low cost, high efficiency, and rapidity, the developed label-free electrochemical biosensor can also be applicable for other Gram-negative bacteria, owning promising potential in the application of portable devices and paving a potential way for the construction of electrochemical biosensors.
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Affiliation(s)
- Sida Ren
- College of Science, Northeastern University, Shenyang, 110004, China
| | - Xi Zhang
- College of Science, Northeastern University, Shenyang, 110004, China
| | - Zhijie Li
- College of Science, Northeastern University, Shenyang, 110004, China
| | - Xiaoxia Jian
- College of Science, Northeastern University, Shenyang, 110004, China
| | - Junjian Zhao
- College of Science, Northeastern University, Shenyang, 110004, China
| | - Yan-Yan Song
- College of Science, Northeastern University, Shenyang, 110004, China.
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Lee SY, Chen F, Lee TY. Tryptamine-functionalized magnetic nanoparticles for highly sensitive detection of Salmonella typhimurium. Analyst 2021; 146:2559-2566. [PMID: 33899066 DOI: 10.1039/d0an02458a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is significant demand for the development of rapid, sensitive, and specific methods for detecting bacterial pathogens in order to identify the causes of food poisoning. Nucleic acid amplification tests (NAATs) allow for the culture-free detection of bacterial pathogens and are not as labor intensive and time consuming as culture-based detection methods. However, suitable sample preparation methods must be developed for the realization of simple, rapid, and sensitive NAATs. To resolve this problem, we developed a new sample preparation method that integrates bacterial pathogen enrichment and DNA extraction. We engineered magnetic nanoparticles (MNPs) with a physicochemical probe (tryptamine) for single-tube sample preparation with minimal sample loss. The tryptamine-functionalized MNPs (Indole@MNPs) showed inherent hydrophobicity owing to the indole side chain and a change in their zeta potential with a decrease in the pH. Because of their physicochemical characteristics, the Indole@MNPs could adsorb bacterial pathogens, thus allowing sample enrichment and DNA binding and release through weak electrostatic interactions via pH control. We successfully detected Salmonella enterica serovar Typhimurium, a common cause of bacterial food poisoning, at a concentration of 10 CFU/10 mL in milk samples using quantitative PCR. Thus, the proposed method allows for the simple and sensitive detection of Salmonella typhimurium and can be used for nontyphoidal salmonella detection to ensure food safety.
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Affiliation(s)
- Seon-Yeong Lee
- Department of Technology Education, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Feixiong Chen
- Department of Convergence System Engineering and Department of Biomedical Engineering, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Tae Yoon Lee
- Department of Technology Education, Chungnam National University, Daejeon, 34134, Republic of Korea and Department of Convergence System Engineering and Department of Biomedical Engineering, Chungnam National University, Daejeon, 34134, Republic of Korea
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