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Liu S, Tian L, Zhang Z, Lu F, Chen S, Ning Y. Fluorometric determination of mecA gene in MRSA with a graphene-oxide based bioassay using flap endonuclease 1-assisted target recycling and Klenow fragment-triggered signal amplification. Int J Biol Macromol 2024; 277:134075. [PMID: 39043285 DOI: 10.1016/j.ijbiomac.2024.134075] [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: 03/17/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium that causes a wide range of illnesses, necessitating the development of new technologies for its detection. Herein, we propose a graphene oxide (GO)-based sensing platform for the detection of mecA gene in MRSA using flap endonuclease 1 (FEN1)-assisted target recycling and Klenow fragment (KF)-triggered signal amplification. Without the target, all the DNA probes were adsorbed onto GO, resulting in fluorescence quenching of the dye. Upon the addition of the target, a triple complex was formed that triggered FEN1-assisted target recycling and initiated two polymerization reactions with the assistance of KF polymerase, generating numerous dsDNA that were repelled by GO. These dsDNAs triggered fluorescence enhancement when SYBR Green I was added. Therefore, the target DNA was quantified by measuring the fluorescence at excitation and emission wavelengths of 480/526 nm. This mecA gene assay showed a good linear range from 1 to 50 nM with a lower limit of detection of 0.26 nM, and displayed good applicability to the analysis of real samples. Thus, a new method for monitoring MRSA has been developed that has great potential for early clinical diagnosis and treatment.
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Affiliation(s)
- Shiwu Liu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, People's Republic of China
| | - Longzhi Tian
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, People's Republic of China
| | - Zidong Zhang
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, People's Republic of China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, People's Republic of China
| | - Shanquan Chen
- Department of General Education, The School of Humanities and Social Science of The Chinese University of Hong Kong (Shenzhen campus), Shenzhen, Guangdong 518172, People's Republic of China.
| | - Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, People's Republic of China.
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2
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Eivazzadeh-Keihan R, Saadatidizaji Z, Mahdavi M, Maleki A, Irani M, Zare I. Recent advances in gold nanoparticles-based biosensors for tuberculosis determination. Talanta 2024; 275:126099. [PMID: 38640517 DOI: 10.1016/j.talanta.2024.126099] [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: 07/28/2023] [Revised: 03/16/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
Tuberculosis (TB) is one of the major killer diseases affecting lung parenchymal tissues. Mycobacterium tuberculosis (Mtb) is the bacterium that causes it. It most commonly affects the lungs, although it can affect any part of the body, including the stomach, glands, bones, and nervous system. Although anti-mycobacterial drugs are available, it remains a major threat to public health due to the rise of drug-resistant strains, and early and accurate diagnosis is very important. Currently, research science and medical communities are focusing on the use of cost-effective biosensors to manage human biological processes and assess accurate health diagnostics. Due to their high sensitivity in chemical and biological assays, nanomaterials have been considered in the field of biosensors for better diagnosis, and among them, gold nanoparticles (AuNPs) can play an important role in accelerating the diagnosis of TB. Superior biocompatibility, conductivity, catalytic properties, high surface-to-volume ratio, and high density enable their widespread use in the fabrication of biosensors. This review evaluates the diagnostic accuracy of AuNP-based biosensors for the detection of Mtb. According to different transducers of biosensors, their structure, performance, advantages and limitations are summarized and compared. Moreover, the upcoming challenges in their analytical performance have been highlighted and the strategies to overcome those challenges have been briefly discussed.
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Affiliation(s)
- Reza Eivazzadeh-Keihan
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran.
| | - Zahra Saadatidizaji
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran.
| | - Mohammad Irani
- Department of Pharmaceutics, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co., Ltd., Shiraz, 7178795844, Iran.
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3
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Jain R, Gupta G, Mitra DK, Guleria R. Diagnosis of extra pulmonary tuberculosis: An update on novel diagnostic approaches. Respir Med 2024; 225:107601. [PMID: 38513873 DOI: 10.1016/j.rmed.2024.107601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
Tuberculosis (TB) remains a major global public health problem worldwide. Though Pulmonary TB (PTB) is mostly discussed, one in five cases of TB present are extrapulmonary TB (EPTB) that manifests conspicuous diagnostic and management challenges with respect to the site of infection. The diagnosis of EPTB is often delayed or even missed due to insidious clinical presentation, pauci-bacillary nature of the disease, and lack of laboratory facilities in the resource limited settings. Culture, the classical gold standard for the diagnosis of tuberculosis, suffers from increased technical and logistical constraints in EPTB cases. Other than culture, several other tests are available but their feasibility and effciacy for the detection of EPTB is still the matter of interest. We need more specific and precise test/s for the various forms of EPTB diagnosis which can easily be applied in the routine TB control program is required. A test that can contribute remarkably towards improving EPTB case detection reducing the morbidity and mortality is the utmost requirement. In this review we described the scenario of molecular and other noval methods available for laboratory diagnosis of EPTB, and also discussed the challenges linked with each diagnostic method. This review will make the readers aware of new emerging diagnostic techniques in the field of EPTB diagnosis. They can make an informed decision to choose the appropriate one according to the test availability, their clinical settings and financial considerations.
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Affiliation(s)
- Rashi Jain
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gopika Gupta
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - D K Mitra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Randeep Guleria
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; Institute of Internal Medicine & Respiratory and Sleep Medicine, Medanta-The Medicity, Gurugram, Haryana, 122033, India.
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4
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Chaturvedi M, Patel M, Tiwari A, Dwivedi N, Mondal DP, Srivastava AK, Dhand C. An insight to the recent advancements in detection of Mycobacterium tuberculosis using biosensors: A systematic review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:14-27. [PMID: 38052326 DOI: 10.1016/j.pbiomolbio.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/31/2023] [Accepted: 10/01/2023] [Indexed: 12/07/2023]
Abstract
Since ancient times, Tuberculosis (TB) has been a severe invasive illness that has been prevalent for thousands of years and is also known as "consumption" or phthisis. TB is the most common chronic lung bacterial illness in the world, killing over 2 million people each year, caused by Mycobacterium tuberculosis (MTB). As per the reports of WHO, in spite of technology advancements, the average rate of decline in global TB infections from 2000-2018 was only 1.6% per year, and the worldwide reduction in TB deaths was only 11%. In addition, COVID-19 pandemic has reversed years of global progress in tackling TB with fewer diagnosed cases. The majority of undiagnosed patients of TB are found in low- and middle-income countries where the GeneXpert MTB/RIF assay and sputum smear microscopy have been approved by the WHO as reference procedures for quickly detecting TB. Biosensors, like other cutting-edge technologies, have piqued researchers' interest since they offer a quick and accurate way to identify MTB. Modern integrated technologies allow for the rapid, low-cost, and highly precise detection of analytes in extremely little amounts of sample by biosensors. Here in this review, we outlined the severity of tuberculosis (TB) and the most recent developments in the biosensors sector, as well as their various kinds and benefits for TB detection. The review also emphasizes how widespread TB is and how it needs accurate diagnosis and effective treatment.
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Affiliation(s)
- Mansi Chaturvedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Monika Patel
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Archana Tiwari
- School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Neeraj Dwivedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - D P Mondal
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Avanish Kumar Srivastava
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Chetna Dhand
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Schmidt K, Hageneder S, Lechner B, Zbiral B, Fossati S, Ahmadi Y, Minunni M, Toca-Herrera JL, Reimhult E, Barisic I, Dostalek J. Rolling Circle Amplification Tailored for Plasmonic Biosensors: From Ensemble to Single-Molecule Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:55017-55027. [PMID: 36446038 PMCID: PMC9756284 DOI: 10.1021/acsami.2c14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
We report on the tailoring of rolling circle amplification (RCA) for affinity biosensors relying on the optical probing of their surface with confined surface plasmon field. Affinity capture of the target analyte at the metallic sensor surface (e.g., by using immunoassays) is followed by the RCA step for subsequent readout based on increased refractive index (surface plasmon resonance, SPR) or RCA-incorporated high number of fluorophores (in surface plasmon-enhanced fluorescence, PEF). By combining SPR and PEF methods, this work investigates the impact of the conformation of long RCA-generated single-stranded DNA (ssDNA) chains to the plasmonic sensor response enhancement. In order to confine the RCA reaction within the evanescent surface plasmon field and hence maximize the sensor response, an interface carrying analyte-capturing molecules and additional guiding ssDNA strands (complementary to the repeating segments of RCA-generated chains) is developed. When using the circular padlock probe as a model target analyte, the PEF readout shows that the reported RCA implementation improves the limit of detection (LOD) from 13 pM to high femtomolar concentration when compared to direct labeling. The respective enhancement factor is of about 2 orders of magnitude, which agrees with the maximum number of fluorophore emitters attached to the RCA chain that is folded in the evanescent surface plasmon field by the developed biointerface. Moreover, the RCA allows facile visualizing of individual binding events by fluorescence microscopy, which enables direct counting of captured molecules. This approach offers a versatile route toward a fast digital readout format of single-molecule detection with further reduced LOD.
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Affiliation(s)
- Katharina Schmidt
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST
Competence Center for Electrochemical Surface Technologies, 3430 Tulln an der
Donau, Austria
| | - Simone Hageneder
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Bernadette Lechner
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST
Competence Center for Electrochemical Surface Technologies, 3430 Tulln an der
Donau, Austria
| | - Barbara Zbiral
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Stefan Fossati
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Yasaman Ahmadi
- Molecular
Diagnostics, Health & Environment, AIT
Austrian Institute of Technology GmbH, 1210 Vienna, Austria
| | - Maria Minunni
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3-13, Sesto Fiorentino, 50019 Firenze, Italy
| | - Jose Luis Toca-Herrera
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Erik Reimhult
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Ivan Barisic
- Molecular
Diagnostics, Health & Environment, AIT
Austrian Institute of Technology GmbH, 1210 Vienna, Austria
| | - Jakub Dostalek
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- FZU-Institute
of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
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6
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Huang T, Zhang R, Li J. CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives. J Adv Res 2022:S2090-1232(22)00240-5. [PMID: 36367481 PMCID: PMC10403697 DOI: 10.1016/j.jare.2022.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements. AIM OF REVIEW This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation. KEY SCIENTIFIC CONCEPTS OF REVIEW Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.
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7
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Joshi H, Kandari D, Maitra SS, Bhatnagar R. Biosensors for the detection of Mycobacterium tuberculosis: a comprehensive overview. Crit Rev Microbiol 2022; 48:784-812. [PMID: 35196464 DOI: 10.1080/1040841x.2022.2035314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Tuberculosis (TB) infection is one of the leading causes of death in the world. According to WHO reports 2019, the average rate of decrease in global TB incidences was only 1.6% per year from 2000 to 2018, besides that the global decline in TB deaths was just 11%. Therefore, the dire need for early detection of the pathogen for the successful diagnosis of TB seems justified. Mycobacterium tuberculosis secretory proteins have gained more attention as TB biomarkers, for the early diagnosis and treatment of TB. Here in this review, we elaborate on the recent advancements made in the field of piezoelectric, magnetic, optical, and electrochemical biosensors, in addition to listing their merits and setbacks. Additionally, this review also discusses the construction of biosensors through modern integrated technologies, such as combinations of analytical chemistry, molecular biology, and nanotechnology. Integrated technologies enhance the detection for perceiving highly selective, specific, and sensitive signals to detect M. tuberculosis. Furthermore, this review highlights the recent challenges and scope of improvement in numerous biosensors developed for rapid, specific, selective, and sensitive detection of tuberculosis to reduce the TB burden and successful treatment.
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Affiliation(s)
- Hemant Joshi
- Laboratory of Molecular biology and Genetic engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Laboratory of Molecular biology and Genetic engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Subhrangsu Sundar Maitra
- Laboratory of Molecular biology and Genetic engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Laboratory of Molecular biology and Genetic engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Amity University of Rajasthan, Jaipur, India
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8
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Niu C, Lin X, Jiang X, Guo F, Liu J, Liu X, Huang H, Huang Y. An electrochemical aptasensor for highly sensitive detection of CEA based on exonuclease III and hybrid chain reaction dual signal amplification. Bioelectrochemistry 2022; 143:107986. [PMID: 34735912 DOI: 10.1016/j.bioelechem.2021.107986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/11/2022]
Abstract
At present, carcinoembryonic antigen (CEA) is considered a broad-spectrum cancer biomarker, and its accurate analysis in clinical samples can assist early cancer diagnosis and treatment. Herein, a novel electrochemical aptasensor has been proposed for CEA detection based on exonuclease III and hybrid chain reaction. The target CEA specifically binds to the aptamer region in hairpin probe 1 (defined as H1) by strong attraction, which leads the rest of the H1 triggering catalytic hairpin assembly to form a high quantity of H1 and hairpin probe 2 (defined as H2) double chain complex (denoted as H1@H2). Subsequently, the exonuclease III digests the complex of H1@H2 and liberates H1 to induce the first signal amplification. Simultaneously, a large number of generated trigger chains initiate a hybrid chain reaction and produce a second signal amplification. This proposed sensor exhibited excellent analytical performance for the detection of CEA, with wide linear range from 10 pg.mL-1 to 100 ng.mL-1 and low limit of detection of 0.84 pg.mL-1. Additionally, the biosensing strategy was successfully verified for direct measurement of CEA in human serum. Therefore, this elaborated sensor provides a new simple method for detecting CEA and exhibits great promise in the early screening of cancer.
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Affiliation(s)
- Cui Niu
- Department of Clinical Laboratory, The Third Hospital of Xingtai, Xingtai, Hebei 054100, China
| | - Xiaojuan Lin
- Department of Clinical Laboratory, The Third Hospital of Xingtai, Xingtai, Hebei 054100, China
| | - Xin Jiang
- Pharmacy Department, Veterans General Hospital of Hebei, Xingtai, Hebei 054100, China
| | - Fei Guo
- Department of Basic Medicine, The Medical College of Xingtai, Xingtai, Hebei 054100, China
| | - Jianxiao Liu
- Department of Clinical Laboratory, The Third Hospital of Xingtai, Xingtai, Hebei 054100, China
| | - Xiangqin Liu
- Department of Clinical Laboratory, The Third Hospital of Xingtai, Xingtai, Hebei 054100, China
| | - Hongge Huang
- Department of Clinical Laboratory, The Third Hospital of Xingtai, Xingtai, Hebei 054100, China
| | - Yu Huang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Science, Beijing 100049, China.
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9
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Zhang J, He F. Mycobacterium tuberculosis piezoelectric sensor based on AuNPs-mediated enzyme assisted signal amplification. Talanta 2022; 236:122902. [PMID: 34635273 DOI: 10.1016/j.talanta.2021.122902] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/13/2021] [Accepted: 09/19/2021] [Indexed: 10/20/2022]
Abstract
Rapid diagnosis of tuberculosis disease (TB) still remained a pressing need for TB control efforts all over the world. However, the existing detection approaches cannot satisfy demand of rapid detection of clinical Mycobacterium tuberculosis (M. tuberculosis) because of the long detection time and high cost. Herein, we proposed a new M. tuberculosis piezoelectric sensor based on AuNPs-mediated enzyme assisted signal amplification. A hairpin-shaped DNA duplex with a protrusion of the 3' end was designed. In the presence of specific 16 S rDNA fragment of M. tuberculosis, the hairpin probe was opened, which triggered the selective cleavage of hairpin probe by Exonuclease III (Exo III), resulting in the release of uncut DNA probe and target DNA. The released target DNA hybridized with another hairpin-shaped DNA duplex, and a new digestion cycle was started, thus generating large amounts of uncut DNA probes. The uncut DNA was pulled to the electrode surface by the hybridization with capture probe modified on the electrode. Subsequently detection probe labeled AuNPs was hybridized with uncut DNA and entered between the two electrodes. The AuNPs linked to hybridized detection probe were grown in the HAuCl4 and Nicotinamide adenine dinucleotide (NADH) solution and offered the conductive connection between the gaps of electrode. The changes were monitored by the piezoelectric sensor. The piezoelectric biosensor could achieve a detection of M. tuberculosis (102-108 CFU mL-1) within 3 h, the detection limit (LOD) was 30 CFU mL-1. The methodology could be transformed into different microbial targets, which is suitable for further development of small portable equipment and multifunctional detection.
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Affiliation(s)
- Jialin Zhang
- Institute of Molecular Materials Chemistry and Technology, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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10
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Lechner B, Hageneder S, Schmidt K, Kreuzer MP, Conzemius R, Reimhult E, Barišić I, Dostalek J. In Situ Monitoring of Rolling Circle Amplification on a Solid Support by Surface Plasmon Resonance and Optical Waveguide Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32352-32362. [PMID: 34212712 DOI: 10.1021/acsami.1c03715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The growth of surface-attached single-stranded deoxyribonucleic acid (ssDNA) chains is monitored in situ using an evanescent wave optical biosensor that combines surface plasmon resonance (SPR) and optical waveguide spectroscopy (OWS). The "grafting-from" growth of ssDNA chains is facilitated by rolling circle amplification (RCA), and the gradual prolongation of ssDNA chains anchored to a gold sensor surface is optically tracked in time. At a sufficient density of the polymer chains, the ssDNA takes on a brush architecture with a thickness exceeding 10 μm, supporting a spectrum of guided optical waves traveling along the metallic sensor surface. The simultaneous probing of this interface with the confined optical field of surface plasmons and additional more delocalized dielectric optical waveguide modes enables accurate in situ measurement of the ssDNA brush thickness, polymer volume content, and density gradients. We report for the first time on the utilization of the SPR/OWS technique for the measurement of the RCA speed on a solid surface that can be compared to that in bulk solutions. In addition, the control of ssDNA brush properties by changing the grafting density and ionic strength and post-modification via affinity reaction with complementary short ssDNA staples is discussed. These observations may provide important leads for tailoring RCA toward sensitive and rapid assays in affinity-based biosensors.
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Affiliation(s)
- Bernadette Lechner
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST Competence Center for Electrochemical Surface Technologies, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Simone Hageneder
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Katharina Schmidt
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Mark P Kreuzer
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- Instituto de Nanosistemas, Universidad Nacional de San Martín, Campus Miguelete, 25 de Mayo 1021, San Martín, CP 1650 Provincia de Buenos Aires, Argentina
| | - Rick Conzemius
- Molecular Diagnostics, Health & Environment, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Erik Reimhult
- Institute for Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 11, Vienna 1190, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Health & Environment, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Jakub Dostalek
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- FZU-Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 182 21, Czech Republic
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11
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Janik M, Hamidi SV, Koba M, Perreault J, Walsh R, Bock WJ, Smietana M. Real-time isothermal DNA amplification monitoring in picoliter volumes using an optical fiber sensor. LAB ON A CHIP 2021; 21:397-404. [PMID: 33331382 DOI: 10.1039/d0lc01069c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rolling circle amplification (RCA) of DNA can be considered as a great alternative to the gold standard polymerase chain reaction (PCR), especially during this pandemic period, where rapid, sensitive, and reliable test results for hundreds of thousands of samples are required daily. This work presents the first research to date on direct, real-time and label-free isothermal DNA amplification monitoring using a microcavity in-line Mach-Zehnder interferometer (μIMZI) fabricated in an optical fiber. The solution based on μIMZI offers a great advantage over many other sensing concepts - making possible optical analysis in just picoliter sample volumes. The selectivity of the biosensor is determined by DNA primers immobilized on the microcavity's surface that act as selective biorecognition elements and trigger initiation of the DNA amplification process. In this study, we verified the sensing concept using circular DNA designed to target the H5N1 influenza virus. The developed biosensor exhibits an ultrahigh refractive index sensitivity reaching 14 000 nm per refractive index unit and a linear detection range between 9.4 aM and 94 pM of the target DNA sequence. Within a 30 min period, the amplification of as little as 9.4 aM DNA can be effectively detected, with a calculated limit of detection of as low as 0.2 aM DNA, suggesting that this methodology holds great promise in practical disease diagnosis applications in the future.
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Affiliation(s)
- Monika Janik
- Warsaw University of Technology, Institute of Microelectronics and Optoelectronics, Koszykowa 75, 00-662, Warszawa, Poland.
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12
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Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring. SENSORS 2021; 21:s21020602. [PMID: 33467078 PMCID: PMC7831002 DOI: 10.3390/s21020602] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.
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13
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Salimiyan Rizi K, Aryan E, Meshkat Z, Ranjbar G, Sankian M, Ghazvini K, Farsiani H, Pourianfar HR, Rezayi M. The overview and perspectives of biosensors and Mycobacterium tuberculosis: A systematic review. J Cell Physiol 2020; 236:1730-1750. [PMID: 32930412 DOI: 10.1002/jcp.30007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) is referred to as a "consumption" or phthisis, which has been a fatal human disease for thousands of years. Mycobacterium tuberculosis (M. tb) might have been responsible for the death of more humans than any other bacterial pathogens. Therefore, the rapid diagnosis of this bacterial infection plays a pivotal role in the timely and appropriate treatment of the patients, as well as the prevention of disease spread. More than 98% of TB cases are reported in developing countries, and due to the lack of well-equipped and specialized diagnostic laboratories, development of effective diagnostic methods based on biosensors is essential for this bacterium. In this review, original articles published in English were retrieved from multiple databases, such as PubMed, Scopus, Google Scholar, Science Direct, and Cochrane Library during January 2010-October 2019. In addition, the reference lists of the articles were also searched. Among 109 electronically searched citations, 42 articles met the inclusion criteria. The highest potential and wide usage of biosensors for the diagnosis of M. tb and its drug resistance belonged to DNA electrochemical biosensors (isoniazid and rifampin strains). Use of biosensors is expanding for the detection of resistant strains of anti-TB antibiotics with high sensitivity and accuracy, while the speed of these sensory methods is considered essential as well. Furthermore, the lowest limit of detection (0.9 fg/ml) from an electrochemical DNA biosensor was based on graphene-modified iron-oxide chitosan hybrid deposited on fluorine tin oxide for the MPT64 antigen target. According to the results, the most common methods used for M. tb detection include acid-fast staining, cultivation, and polymerase chain reaction (PCR). Although molecular techniques (e.g., PCR and real-time PCR) are rapid and sensitive, they require sophisticated laboratory and apparatuses, as well as skilled personnel and expertise in the commentary of the results. Biosensors are fast, valid, and cost-efficient diagnostic method, and the improvement of their quality is of paramount importance in resource-constrained settings.
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Affiliation(s)
- Kobra Salimiyan Rizi
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Aryan
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Golnaz Ranjbar
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Division of Immunobiochemistry, Immunology Research Centre, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Farsiani
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid R Pourianfar
- Research Department of Industrial Fungi Biotechnology, Research Institute for Industrial Biotechnology, Academic Centre for Education, Culture and Research [ACECR]-Khorasan Razavi Province Branch, Mashhad, Iran
| | - Majid Rezayi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Tian B, Gao F, Fock J, Dufva M, Hansen MF. Homogeneous circle-to-circle amplification for real-time optomagnetic detection of SARS-CoV-2 RdRp coding sequence. Biosens Bioelectron 2020; 165:112356. [PMID: 32510339 DOI: 10.1016/j.bios.2020.112356] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Abstract
Circle-to-circle amplification (C2CA) is a specific and precise cascade nucleic acid amplification method consisting of more than one round of padlock probe ligation and rolling circle amplification (RCA). Although C2CA provides a high amplification efficiency with a negligible increase of false-positive risk, it contains several step-by-step operation processes. We herein demonstrate a homogeneous and isothermal nucleic acid quantification strategy based on C2CA and optomagnetic analysis of magnetic nanoparticle (MNP) assembly. The proposed homogeneous circle-to-circle amplification eliminates the need for additional monomerization and ligation steps after the first round of RCA, and combines two amplification rounds in a one-pot reaction. The second round of RCA produces amplicon coils that anneal to detection probes grafted onto MNPs, resulting in MNP assembly that can be detected in real-time using an optomagnetic sensor. The proposed methodology was applied for the detection of a synthetic complementary DNA of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2, also known as 2019-nCoV) RdRp (RNA-dependent RNA polymerase) coding sequence, achieving a detection limit of 0.4 fM with a dynamic detection range of 3 orders of magnitude and a total assay time of ca. 100 min. A mathematical model was set up and validated to predict the assay performance. Moreover, the proposed method was specific to distinguish SARS-CoV and SARS-CoV-2 sequences with high similarity.
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Affiliation(s)
- Bo Tian
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800, Kongens Lyngby, Denmark.
| | - Fei Gao
- Department of Physics, Technical University of Denmark, DTU Physics, Building 307, DK-2800, Kongens Lyngby, Denmark
| | - Jeppe Fock
- Blusense Diagnostics ApS, Fruebjergvej 3, DK-2100, Copenhagen, Denmark
| | - Martin Dufva
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800, Kongens Lyngby, Denmark
| | - Mikkel Fougt Hansen
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800, Kongens Lyngby, Denmark.
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15
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He H, Xia X, Yang H, Peng Q, Zheng J. A pilot study: a possible implication of Candida as an etiologically endogenous pathogen for oral lichen planus. BMC Oral Health 2020; 20:72. [PMID: 32171292 PMCID: PMC7071738 DOI: 10.1186/s12903-020-1042-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/10/2020] [Indexed: 02/03/2023] Open
Abstract
Background The aim of this study was to investigate the prevalence and genotypic profiles of Candida albicans in patients with oral lichen planus (OLP). Materials and methods Positive rates and genotypic profiles of Candida albicans strains from OLP patients and healthy controls were analyzed. Random amplified polymorphic DNA and internal transcribed spacer of ribosome DNA polymerase chain reactions were used to sequence the DNA of these strains, and then their genetic similarity was measured using BLAST, UIV Band, and Vector NTI Suite Sequence Analyses Software. Results The prevalence of C. albicans strains detected from erosive-OLP, non-erosive OLP, and normal individuals was 18.87, 18.75, and 7.92%, respectively. Four different genotypes were revealed by the two methods. To be specific, type I was found only in the healthy subjects; type II a and II b were found in non-erosive OLP, and type III was identified in erosive OLP. Intragroup similarity coefficients, i.e. SAB were 100%, and inter-groups similarity coefficients, i.e. SAB were less than 30%. Conclusions The genotypic results of C. albicans in OLP revealed an endogenous rather than exogenous infection of C. albicans. In addition, a possible pathogenic role of C. albicans in OLP, with the etiologic sense contributing to a more proper recognition on the pathogenesis, development, and progression of OLP, as well as some strategies for its diagnosis and treatment were identified.
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Affiliation(s)
- Hong He
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China. .,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, China.
| | - Xinyu Xia
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China
| | - Haiping Yang
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, China
| | - Qiao Peng
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaoer Zheng
- The Affiliated Stomatology Hospital, Zhejiang University School of Medicine, Yan'an Road, Hangzhou, 310006, China. .,Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, China.
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16
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Li Y, Wang J, Wang S, Wang J. Rolling circle amplification based colorimetric determination of Staphylococcus aureus. Mikrochim Acta 2020; 187:119. [PMID: 31927667 DOI: 10.1007/s00604-019-4082-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 12/10/2019] [Indexed: 11/30/2022]
Abstract
A colorimetric microplate assay for determination of Staphylococcus aureus DNA is described. Linear padlock probes were designed to recognize target sequences. After DNA binding, the linear padlock probes were circularized by ligation and then hybridize with biotin-labeled capture probes. Biotin-labeled capture probes act as primers to initiate the RCA. The biotin-labeled RCA products hybridize with digoxin-labeled signal probes fixed on streptavidin-functionalized wells of a 96-well plate. To enhance sensitivity, an AuNP-anti-digoxigenin-POx-HRP conjugate was added to the wells and then bound to digoxin-labeled signalling probes. The oxidation of tetramethylbenzidine (TMB) by H2O2 produces a color change from colorless to blue via HRP catalysis. After the reaction was terminated, absorbance is measured at 450 nm. For target sequences of Staphylococcus aureus, the detection limit is 1.2 pM. For genomic DNA, the detection limit is 7.4 pg.μL-1. The potential application of the method was verified by analyzing spiked food samples. Graphical abstractSchematic representation of rolling circle amplification and functionalized AuNP-based colorimetric determination of Staphylococcus aureus. The method uses streptavidin-functionalized 96-well plates and RCA as a molecular tool and AuNP-anti-digoxigenin-POx-HRP as signal transduction markers to increase sensitivity.
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Affiliation(s)
- Yanan Li
- State Key Laboratory for Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, 29 The Thirteenth Road, Tianjin Economy and Technology Development Area, Tianjin, 300457, People's Republic of China
| | - Junying Wang
- Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Haidian District, Beijing, 010010, People's Republic of China
| | - Shuo Wang
- Medical college, Nankai University, No.38 Tongyan Road, Jinnan District, Tianjin, 300350, People's Republic of China.
| | - Junping Wang
- State Key Laboratory for Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, 29 The Thirteenth Road, Tianjin Economy and Technology Development Area, Tianjin, 300457, People's Republic of China.
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Yang K, Yu W, Huang G, Zhou J, Yang X, Fu W. Highly sensitive detection of Staphylococcus aureus by a THz metamaterial biosensor based on gold nanoparticles and rolling circle amplification. RSC Adv 2020; 10:26824-26833. [PMID: 35515811 PMCID: PMC9055468 DOI: 10.1039/d0ra03116j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/09/2020] [Indexed: 01/31/2023] Open
Abstract
A highly sensitive method for detecting Staphylococcus aureus (S. aureus) is urgently needed to reduce the impact and spread of hospital-acquired infections and food-borne illness. For this purpose, this paper presents a THz metamaterial biosensor based on gold nanoparticles (AuNPs) and rolling circle amplification (RCA). The RCA process amplified the S. aureus DNA fragments and generated copious yields of long single-strand DNA molecules. These molecules were then conjugated with the AuNPs to form complexes that delivered exceptional increases in the refractive indices of the samples, and resulted in corresponding improvements in the THz response of the metamaterial. Under optimal conditions, the shifts in the metamaterial's resonance frequency displayed a linear relationship with concentrations of synthetic S. aureus DNA in the range from 10 fM to 10 pM, with a limit of detection of 2.77 fM. We also tested the practical application of this biosensor in measurements of genomic DNA in clinical bacterial strains, where the sensor showed a detection limit of 0.08 pg μL−1 and a linear range from 0.1 to 5 pg μL−1. It also exhibited reasonable specificity, resisting interference from three other pathogenic bacteria. These findings indicate that the proposed approach offers a cost-effective THz biosensing strategy that can be easily fabricated and conveniently operated to aid the diagnosis of infectious disease and food safety control. A highly sensitive method for detecting Staphylococcus aureus (S. aureus) is urgently needed to reduce the impact and spread of hospital-acquired infections and food-borne illness.![]()
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Affiliation(s)
- Ke Yang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University (Army Medical University)
- Chongqing 400038
- China
| | - Wenjing Yu
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University (Army Medical University)
- Chongqing 400038
- China
| | - Guorong Huang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University (Army Medical University)
- Chongqing 400038
- China
| | - Jie Zhou
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University (Army Medical University)
- Chongqing 400038
- China
| | - Xiang Yang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University (Army Medical University)
- Chongqing 400038
- China
| | - Weiling Fu
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University (Army Medical University)
- Chongqing 400038
- China
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18
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DNA markers and nano-biosensing approaches for tuberculosis diagnosis. NANOTECHNOLOGY BASED APPROACHES FOR TUBERCULOSIS TREATMENT 2020. [PMCID: PMC7303904 DOI: 10.1016/b978-0-12-819811-7.00013-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
According to WHO 2018 report, 10 million people developed tuberculosis and 1.3 million died from it making it 1 of 10 deadliest diseases worldwide. Tuberculosis is caused by infection with the bacillus Mycobacterium tuberculosis (Mtb). WHO recommends using a specific diagnostic kit Xpert MTB/RIF developed by Cepheid (California, United States). An alarming number of new cases (ca. 558,000) of rifampicin-resistant tuberculosis was diagnosticated in 2017. In recent years, new diagnosis tools targeting the Mtb DNA biomarkers have emerged using a plethora of nanomaterials capable of delivering new technological approaches for the rapid diagnostics of TB and rifampicin-resistant TB (RR-TB). In this chapter, we summarized the state-of-the-art of the current available DNA biomarkers and the potential applications for the development of new diagnosis nanotechnology-based devices. The latter use carbonaceous nanomaterials (graphene and carbon nanotubes), noble metals (silver and gold), semi-conducting (metal oxides, magnetic beads, and quantum dots) in order to reveal and/or to amplify the signal after the recognition of target DNA biomarker. The readout techniques such as colorimetry, fluorescence, surface plasmon resonance, and electrochemical methods were also reviewed. Future is bright for point-of-care diagnostics with a sample-in answer-out approach that hampers user-error through miniaturization of biochip technology to the nanoscale range, which will enable their use by nonspecialized personnel.
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19
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Huertas CS, Calvo-Lozano O, Mitchell A, Lechuga LM. Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective. Front Chem 2019; 7:724. [PMID: 31709240 PMCID: PMC6823211 DOI: 10.3389/fchem.2019.00724] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
Evanescent-wave optical biosensors have become an attractive alternative for the screening of nucleic acids in the clinical context. They possess highly sensitive transducers able to perform detection of a wide range of nucleic acid-based biomarkers without the need of any label or marker. These optical biosensor platforms are very versatile, allowing the incorporation of an almost limitless range of biorecognition probes precisely and robustly adhered to the sensor surface by covalent surface chemistry approaches. In addition, their application can be further enhanced by their combination with different processes, thanks to their integration with complex and automated microfluidic systems, facilitating the development of multiplexed and user-friendly platforms. The objective of this work is to provide a comprehensive synopsis of cutting-edge analytical strategies based on these label-free optical biosensors able to deal with the drawbacks related to DNA and RNA detection, from single point mutations assays and epigenetic alterations, to bacterial infections. Several plasmonic and silicon photonic-based biosensors are described together with their most recent applications in this area. We also identify and analyse the main challenges faced when attempting to harness this technology and how several innovative approaches introduced in the last years manage those issues, including the use of new biorecognition probes, surface functionalization approaches, signal amplification and enhancement strategies, as well as, sophisticated microfluidic solutions.
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Affiliation(s)
- Cesar S. Huertas
- Integrated Photonics and Applications Centre, School of Engineering, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
| | - Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and the Barcelona Institute of Science and Technology, CIBER-BBN, Barcelona, Spain
| | - Arnan Mitchell
- Integrated Photonics and Applications Centre, School of Engineering, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and the Barcelona Institute of Science and Technology, CIBER-BBN, Barcelona, Spain
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20
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Plasmonic-based platforms for diagnosis of infectious diseases at the point-of-care. Biotechnol Adv 2019; 37:107440. [PMID: 31476421 DOI: 10.1016/j.biotechadv.2019.107440] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/21/2019] [Indexed: 12/17/2022]
Abstract
Infectious diseases such as HIV-1/AIDS, tuberculosis (TB), hepatitis B (HBV), and malaria still exert a tremendous health burden on the developing world, requiring rapid, simple and inexpensive diagnostics for on-site diagnosis and treatment monitoring. However, traditional diagnostic methods such as nucleic acid tests (NATs) and enzyme linked immunosorbent assays (ELISA) cannot be readily implemented in point-of-care (POC) settings. Recently, plasmonic-based biosensors have emerged, offering an attractive solution to manage infectious diseases in the developing world since they can achieve rapid, real-time and label-free detection of various pathogenic biomarkers. Via the principle of plasmonic-based optical detection, a variety of biosensing technologies such as surface plasmon resonance (SPR), localized surface plasmon resonance (LSPR), colorimetric plasmonic assays, and surface enhanced Raman spectroscopy (SERS) have emerged for early diagnosis of HIV-1, TB, HBV and malaria. Similarly, plasmonic-based colorimetric assays have also been developed with the capability of multiplexing and cellphone integration, which is well suited for POC testing in the developing world. Herein, we present a comprehensive review on recent advances in surface chemistry, substrate fabrication, and microfluidic integration for the development of plasmonic-based biosensors, aiming at rapid management of infectious diseases at the POC, and thus improving global health.
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21
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Ultrasensitive Real-Time Rolling Circle Amplification Detection Enhanced by Nicking-Induced Tandem-Acting Polymerases. Anal Chem 2019; 91:10102-10109. [DOI: 10.1021/acs.analchem.9b02073] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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Abstract
Biosensors based on the principle of surface plasmon resonance (SPR) are surface-sensitive optical devices used for monitoring biomolecular interactions at the sensor surface in real time without any labeling. It is used in a wide variety of areas including proteomics, clinical diagnosis, environmental monitoring, drug discovery, and food analysis. C-reactive protein (CRP) is a marker of inflammation, which undergoes conformation changes in local lesions, leading to the formation of mCRP. Autoantibodies against mCRP are frequently detected in systemic lupus erythematosus (SLE) and associated with disease activity and prognosis. An SPR immunoassay for CRP autoantibodies at complement factor H-CRP interface is described in this chapter.
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Affiliation(s)
- Qiu-Yu Li
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital, Beijing, People's Republic of China.
| | - Hai-Yun Li
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
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23
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Rastogi M, Singh SK. Advances in Molecular Diagnostic Approaches for Biothreat Agents. DEFENSE AGAINST BIOLOGICAL ATTACKS 2019. [PMCID: PMC7123646 DOI: 10.1007/978-3-030-03071-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The advancement in Molecular techniques has been implicated in the development of sophisticated, high-end diagnostic platform and point-of-care (POC) devices for the detection of biothreat agents. Different molecular and immunological approaches such as Immunochromatographic and lateral flow assays, Enzyme-linked Immunosorbent assays (ELISA), Biosensors, Isothermal amplification assays, Nucleic acid amplification tests (NAATs), Next Generation Sequencers (NGS), Microarrays and Microfluidics have been used for a long time as detection strategies of the biothreat agents. In addition, several point of care (POC) devices have been approved by FDA and commercialized in markets. The high-end molecular platforms like NGS and Microarray are time-consuming, costly, and produce huge amount of data. Therefore, the future prospects of molecular based technique should focus on developing quick, user-friendly, cost-effective and portable devices against biological attacks and surveillance programs.
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Li S, Liu X, Pang S, Lu R, Liu Y, Fan M, Jia Z, Bai H. Voltammetric determination of DNA based on regulation of DNA strand displacement using an allosteric DNA toehold. Mikrochim Acta 2018; 185:433. [DOI: 10.1007/s00604-018-2967-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 08/18/2018] [Indexed: 01/07/2023]
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25
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Nakano S, Nagao M, Yamasaki T, Morimura H, Hama N, Iijima Y, Shinomiya H, Tanaka M, Yamamoto M, Matsumura Y, Miyake S, Ichiyama S. Evaluation of a surface plasmon resonance imaging-based multiplex O-antigen serogrouping for Escherichia coli using eleven major serotypes of Shiga -toxin-producing E. coli. J Infect Chemother 2018; 24:443-448. [DOI: 10.1016/j.jiac.2018.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/28/2017] [Accepted: 01/17/2018] [Indexed: 02/02/2023]
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26
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Kerry RG, Gouda S, Sil B, Das G, Shin HS, Ghodake G, Patra JK. Cure of tuberculosis using nanotechnology: An overview. J Microbiol 2018; 56:287-299. [PMID: 29721825 DOI: 10.1007/s12275-018-7414-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 02/03/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), a major health issue of the present era. The bacterium inhabits the host macrophage and other immune cells where it modulates the lysosome trafficking protein, hinders the formation of phagolysosome, and blocks the TNF receptor-dependent apoptosis of host macrophage/monocytes. Other limitations such as resistance to and low bioavailability and bio-distribution of conventional drugs aid to their high virulence and human mortality. This review highlights the use of nanotechnology-based approaches for drug formulation and delivery which could open new avenues to limit the pathogenicity of tuberculosis. Moreover phytochemicals, such as alkaloids, phenols, saponins, steroids, tannins, and terpenoids, extracted from terrestrial plants and mangroves seem promising against M. tuberculosis through different molecular mechanisms. Further understanding of the genomics and proteomics of this pathogenic microbe could also help overcome various research gaps in the path of developing a suitable therapy against tuberculosis.
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Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, AMIT College, Khurda, 752057, Odisha, India
| | - Sushanto Gouda
- Amity Institute of Wildlife Science, Amity University, Noida, 201313, Uttar Pradesh, India
| | - Bikram Sil
- Department of Biotechnology, AMIT College, Khurda, 752057, Odisha, India
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Han-Seung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
| | - Gajanan Ghodake
- Department of Biological and Environmental Science, College of Life Science and Biotechnology, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Chen Z, Duan X, Wei H, Tang S, Xu C, Li Y, Guan Y, Zhao G. Screening oligonucleotide sequences for silver staining and d-galactose visual detection using RCA silver staining in a tube. Acta Biochim Biophys Sin (Shanghai) 2018; 50:507-515. [PMID: 29635339 DOI: 10.1093/abbs/gmy034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 03/07/2018] [Indexed: 02/04/2023] Open
Abstract
Oligonucleotides were screened for strongly silver-stained repetitive sequences. An 'AG'-clustered purine sequence showed strong staining, and the staining density can be compromised by disrupting the continuity of the 'AG'-clustered sequence. The staining-favored sequence was then employed in rolling circle amplification (RCA) for its product detection. A tube-staining method was developed for convenient and visual RCA assay. Moreover, by introducing GalR into RCA, d-galactose was detected by RCA tube-staining with naked eyes without any equipment. About 10 mM d-galactose can be easily identified, and the detection of d-galactose was specific in comparison with that of several other monosaccharides.
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Affiliation(s)
- Ziwei Chen
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Xuying Duan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Hua Wei
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Chidong Xu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yanlei Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, China
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28
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Lee CY, Kang KS, Park KS, Park HG. Determination of RNase H activity via real-time monitoring of target-triggered rolling circle amplification. Mikrochim Acta 2017; 185:53. [DOI: 10.1007/s00604-017-2610-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
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Highly sensitive surface plasmon resonance biosensor for the detection of HIV-related DNA based on dynamic and structural DNA nanodevices. Biosens Bioelectron 2017; 100:228-234. [PMID: 28918231 DOI: 10.1016/j.bios.2017.08.042] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/09/2017] [Accepted: 08/17/2017] [Indexed: 01/23/2023]
Abstract
Early detection, diagnosis and treatment of human immune deficiency virus (HIV) infection is the key to reduce acquired immunodeficiency syndrome (AIDS) mortality. In our research, an innovative surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of HIV-related DNA based on entropy-driven strand displacement reactions (ESDRs) and double-layer DNA tetrahedrons (DDTs). ESDRs as enzyme-free and label-free signal amplification circuit can be specifically triggered by target DNA, leading to the cyclic utilization of target DNA and the formation of plentiful double-stranded DNA (dsDNA) products. Subsequently, the dsDNA products bind to the immobilized hairpin capture probes and further combine with DDTs nanostructures. Due to the high efficiency of ESDRs and large molecular weight of DDTs, the SPR response signal was enhanced dramatically. The proposed SPR biosensor could detect target DNA sensitively and specifically in a linear range from 1pM to 150nM with a detection limit of 48fM. In addition, the whole detecting process can be accomplished in 60min with high accuracy and duplicability. In particular, the developed SPR biosensor was successfully used to analyze target DNA in complex biological sample, indicating that the developed strategy is promising for rapid and early clinical diagnosis of HIV infection.
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30
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Yu R, Shibayama T, Ishioka J, Meng X, Lei Y, Watanabe S. Plasmonic surface nanostructuring of Au-dots@SiO 2 via laser-irradiation induced dewetting. NANOTECHNOLOGY 2017; 28:275701. [PMID: 28541250 DOI: 10.1088/1361-6528/aa74f7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The in situ observation of Au dot formation and the self-assembly dynamics of Au nanoparticles (NPs) was successfully demonstrated via dewetting of Au thin films on SiO2 glass substrates under nano-second pulsed laser irradiation using a multi-quantum beam high-voltage electron microscope. Moreover, using electron energy-loss spectroscopy (EELS) performed in a scanning transmission electron microscope (STEM), the plasmonic properties of the formed Au/SiO2 nanostructure were analyzed to demonstrate its validity in advanced optical devices. The uniformly distributed Au NPs evolved into a dot alignment through movement and coalescence processes was demonstrated in this in situ observation. We carried out the plasmon-loss images of the plan view and the cross-section of the Au/SiO2 nanostructures were obtained at the plasmon-loss peak energy for investigate the three-dimensional distribution of surface plasmon. Furthermore, discrete-dipole approximation (DDA) calculations were used to simulate the plasmonic properties, such as the surface plasmon resonance and the surface plasmon field distribution, of isolated single Au/SiO2 nanostructures. This STEM-EELS-acquired surface plasmon map of the cross-sectional sample is in excellent agreement with the DDA calculations. This results demonstrated the influence of the contact condition between Au NP and SiO2 glass on the plasmonic properties, and may improve the technology for developing advanced optical devices.
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Affiliation(s)
- Ruixuan Yu
- Center for Advanced Research of Energy and Materials, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
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31
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El-Samadony H, Althani A, Tageldin MA, Azzazy HME. Nanodiagnostics for tuberculosis detection. Expert Rev Mol Diagn 2017; 17:427-443. [PMID: 28317400 DOI: 10.1080/14737159.2017.1308825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is a leading killer worldwide. End TB strategy aims at ending the TB epidemic by 2030. Early, accurate, and affordable diagnosis represents a cornerstone to achieve this goal. Innovative strategies for TB diagnostics have been introduced. However, the ideal assay is yet unavailable and conventional methods remain necessary for diagnosis. Unique properties of nanoparticles (NPs) have allowed their utilization in TB detection via targeting disease biomarkers. Area covered: Until now, around thirty-five TB NP-based assays have been partially or fully characterized. Accuracy, low-cost, and short time-to-result represent the common properties of proposed platforms. TB nanodiagnostics now encompass almost all clinical aspects of the disease including active TB, non-tuberculous mycobacteria, rifampicin resistant TB, TB/HIV co-infection, latent TB, and extra-pulmonary TB. This review summarizes state-of-the-art knowledge of TB nanodiagnostics for the last 10 years. Special consideration is given for fabrication concepts, detection strategies, and clinical performance using various clinical specimens. The potential of TB nanodiagnostics to fulfill the need for ideal MTB testing is assessed. Expert commentary: TB nanodiagnostics show promise to be ideal detection tools that can meet the rigorous demands to end the TB epidemic by 2030.
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Affiliation(s)
| | - Asma Althani
- b Health Sciences Department, College of Arts and Sciences , Qatar University , Doha , Qatar
| | - Mohamed Awad Tageldin
- c Department of Chest Diseases, Faculty of Medicine , Ain Shams University , Cairo , Egypt
| | - Hassan M E Azzazy
- d Department of Chemistry, School of Sciences & Engineering , the American University in Cairo , New Cairo , Egypt
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32
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Fu W, Wei S, Wang C, Du Z, Zhu P, Wu X, Wu G, Zhu S. A temperature-tolerant multiplex elements and genes screening system for genetically modified organisms based on dual priming oligonucleotide primers and capillary electrophoresis. Food Chem 2017; 229:396-402. [PMID: 28372191 DOI: 10.1016/j.foodchem.2017.02.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/17/2016] [Accepted: 02/17/2017] [Indexed: 01/22/2023]
Abstract
High throughput screening systems are the preferred solution to meet the urgent requirement of increasing number of genetically modified organisms (GMOs). In this study, we have successfully developed a multiplex GMO element screening system with dual priming oligonucleotide (DPO) primers. This system can detect the cauliflower mosaic virus 35S (CaMV 35S), terminator of nopaline synthase gene (NOS), figwort mosaic virus 35S (FMV 35S) promoter, neomycin phosphotransferaseII (NPTII), Bt Cry 1Ab, phosphinothricin acetyltransferase genes (bar) and Streptomyces viridochromogenes (pat) simultaneously, which covers more than 90% of all authorized GMO species worldwide. This system exhibits a high tolerance to annealing temperatures, high specificity and a limit of detection equal to conventional PCR. A total of 214 samples from markets, national entry-exit agencies, the Institute for Reference Materials and Measurement (IRMM) and the American Oil Chemists' Society (AOCS) were also tested for applicability. This screening system is therefore suitable for GMO screening.
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Affiliation(s)
- Wei Fu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuang Wei
- Shantou Entry-exit Inspection and Quarantine Bureau, Shantou 515041, China
| | - Chenguang Wang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhixin Du
- Guangxi Entry-exit Inspection and Quarantine Bureau, Nanning 530028, China
| | - Pengyu Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xiyang Wu
- Department of Food Science and Engineering, College of Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gang Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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33
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Hao K, He Y, Lu H, Pu S, Zhang Y, Dong H, Zhang X. High-sensitive surface plasmon resonance microRNA biosensor based on streptavidin functionalized gold nanorods-assisted signal amplification. Anal Chim Acta 2017; 954:114-120. [PMID: 28081805 DOI: 10.1016/j.aca.2016.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 01/25/2023]
Abstract
Herein, a facile and sensitive microRNA (miRNA) biosensor was designed by using interfacial biotinylated thiolated DNA molecular beacon (MB) as probe and streptavidin functionalized gold nanorods (Stre-GNRs) as tag for the enhanced surface plasmon resonance (SPR) signal. The MB probe with two terminals labeled with biotin and thiol groups, respectively, was modified on the gold film via thiol-gold interaction. Upon hybridization with the target, the biotinylated group became accessible to the Stre-GNRs. The introduction of the Stre-GNRs tag to the gold film produced strong SPR signal for detection. Our work has illustrated that the plasmonic field extension generated from the gold film to GNRs and the mass increase due to the GNRs have led to drastic sensitivity enhancement. Under optimal conditions, this proposed approach allowed detection of miRNA with the limit of detection (LOD) down to 0.045 pM. The results have shown that the MB probe functionalized sensing film, together with streptavidin-conjugated GNRs, was readily served as a plasmonic coupling partner that can be used as a powerful ultrasensitive sandwich assay for miRNA detection, and GNRs were readily served as promising amplification labels in SPR sensing technology.
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Affiliation(s)
- Kaihong Hao
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Yu He
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Huiting Lu
- School of Space and Environment, Beihang University, Beijing, 100191, PR China
| | - Shaotao Pu
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Yingnan Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
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34
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Yang X, Yang K, Zhao X, Lin Z, Liu Z, Luo S, Zhang Y, Wang Y, Fu W. Terahertz spectroscopy for the isothermal detection of bacterial DNA by magnetic bead-based rolling circle amplification. Analyst 2017; 142:4661-4669. [PMID: 29119154 DOI: 10.1039/c7an01438d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A terahertz biosensor based on rolling circle amplification was developed for the isothermal detection of bacterial DNA.
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Affiliation(s)
- Xiang Yang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Ke Yang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Xiang Zhao
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Zhongquan Lin
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Zhiyong Liu
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Sha Luo
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Yang Zhang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Yunxia Wang
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
| | - Weiling Fu
- Department of Laboratory Medicine
- Southwest Hospital
- Third Military Medical University
- Chongqing 400038
- China
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35
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Wei H, Hu B, Tang S, Zhao G, Guan Y. Repressor logic modules assembled by rolling circle amplification platform to construct a set of logic gates. Sci Rep 2016; 6:37477. [PMID: 27869177 PMCID: PMC5116584 DOI: 10.1038/srep37477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/28/2016] [Indexed: 12/27/2022] Open
Abstract
Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully. To achieve various logic computations based on these basic modules, we designed series and parallel strategies of circular templates, which can further assemble these repressor modules in an RCA platform to realize twelve two-input Boolean logic gates and a three-input logic gate. The RCA-output and RCA-assembled platform was proved to be easy and flexible for complex logic processes and might have application potential in molecular computing and synthetic biology.
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Affiliation(s)
- Hua Wei
- Animal Science and Veterinary Medicine College, Shenyang Agricultural University, #120 Dongling Road, Shenyang, Liaoning, 110866, China.,Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Bo Hu
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
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36
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A SPR biosensor based on signal amplification using antibody-QD conjugates for quantitative determination of multiple tumor markers. Sci Rep 2016; 6:33140. [PMID: 27615417 PMCID: PMC5018874 DOI: 10.1038/srep33140] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022] Open
Abstract
The detection of tumor markers is very important in early cancer diagnosis; however, tumor markers are usually present at very low concentrations, especially in the early stages of tumor development. Surface plasmon resonance (SPR) is widely used to detect biomolecular interactions; it has inherent advantages of being high-throughput, real-time, and label-free technique. However, its sensitivity needs essential improvement for practical applications. In this study, we developed a signal amplification strategy using antibody-quantum dot (QD) conjugates for the sensitive and quantitative detection of α-fetoprotein (AFP), carcinoembryonic antigen (CEA) and cytokeratin fragment 21-1 (CYFRA 21-1) in clinical samples. The use of a dual signal amplification strategy using AuNP-antibody and antibody-QD conjugates increased the signal amplification by 50-folds. The constructed SPR biosensor showed a detection limit as low as 0.1 ng/mL for AFP, CEA, and CYFRA 21-1. Moreover, the results obtained using this SPR biosensor were consistent with those obtained using the electrochemiluminescence method. Thus, the constructed SPR biosensor provides a highly sensitive and specific approach for the detection of tumor markers. This SPR biosensor can be expected to be readily applied for the detection of other tumor markers and can offer a potentially powerful solution for tumor screening.
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Ding X, Cheng W, Li Y, Wu J, Li X, Cheng Q, Ding S. An enzyme-free surface plasmon resonance biosensing strategy for detection of DNA and small molecule based on nonlinear hybridization chain reaction. Biosens Bioelectron 2016; 87:345-351. [PMID: 27587359 DOI: 10.1016/j.bios.2016.08.077] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023]
Abstract
A label-free and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive and specific detection of target DNA by employing the nonlinear hybridization chain reaction (HCR) amplification. Nonlinear HCR is a hairpin-free system in which double-stranded DNA monomers could dendritically assemble into highly branched nanostructure upon introducing a trigger sequence. The target DNA partly hybridizes with capture probe on the gold sensing chip and the unpaired fragment of target DNA works as a trigger to initiate the nonlinear HCR, forming a chain-branching growth of DNA dendrimer by self-assembly. Real-time amplified SPR response is observed upon the introduction of nonlinear HCR system. The method is capable of detecting target DNA at the concentration down to 0.85 pM in 60min with a dynamic range from 1 pM to 1000 pM, and could discriminate target DNA from mismatched sequences. This biosensing strategy exhibits good reproducibility and precision, and has been successfully applied for detection of target DNA in complex sample matrices. In addition, the nonlinear HCR based SPR biosensing methodology is extended to the detection of adenosine triphosphate (ATP) by aptamer recognition. Thus, the versatile method might become a potential alternative tool for biomolecule detection in medical research and early clinical diagnosis.
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Affiliation(s)
- Xiaojuan Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; Molecular Oncology and Epigenetics Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yujian Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiangling Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Quan Cheng
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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38
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Goo NI, Kim DE. Rolling circle amplification as isothermal gene amplification in molecular diagnostics. BIOCHIP JOURNAL 2016; 10:262-271. [PMID: 32226587 PMCID: PMC7096790 DOI: 10.1007/s13206-016-0402-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022]
Abstract
Rolling circle amplification (RCA) developed in the mid-1990s has been widely used as an efficient isothermal DNA amplification process for molecular diagnosis. This enzymatic process amplifies target DNA sequences with high fidelity and specificity by using the strand displacing DNA polymerases. The product of RCA is long single-stranded DNA that contains tandem repeat of target sequence. Isothermal reaction amplification condition of RCA has an advantage over conventional polymerase chain reaction, because no temperature cycling devices are needed for RCA. Thus, RCA is suitable tool for point-of-care detection of target nucleic acids as well as facile detection of target genes. Combined with various detection methods, RCA could amplify and detect femtomolar scale of target nucleic acids with a specificity of one or two base discrimination. Herein, RCA technology is reviewed with an emphasis on molecular diagnosis of microRNAs, infectious pathogens, and point mutations.
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Affiliation(s)
- Nam-In Goo
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029 Korea
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39
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Quantum dot monolayer for surface plasmon resonance signal enhancement and DNA hybridization detection. Biosens Bioelectron 2016; 80:477-482. [DOI: 10.1016/j.bios.2016.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/27/2016] [Accepted: 02/05/2016] [Indexed: 01/05/2023]
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40
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Zhu X, Li J, He H, Huang M, Zhang X, Wang S. Application of nanomaterials in the bioanalytical detection of disease-related genes. Biosens Bioelectron 2015; 74:113-33. [PMID: 26134290 DOI: 10.1016/j.bios.2015.04.069] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/09/2015] [Accepted: 04/21/2015] [Indexed: 12/15/2022]
Abstract
In the diagnosis of genetic diseases and disorders, nanomaterials-based gene detection systems have significant advantages over conventional diagnostic systems in terms of simplicity, sensitivity, specificity, and portability. In this review, we describe the application of nanomaterials for disease-related genes detection in different methods excluding PCR-related method, such as colorimetry, fluorescence-based methods, electrochemistry, microarray methods, surface-enhanced Raman spectroscopy (SERS), quartz crystal microbalance (QCM) methods, and dynamic light scattering (DLS). The most commonly used nanomaterials are gold, silver, carbon and semiconducting nanoparticles. Various nanomaterials-based gene detection methods are introduced, their respective advantages are discussed, and selected examples are provided to illustrate the properties of these nanomaterials and their emerging applications for the detection of specific nucleic acid sequences.
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Affiliation(s)
- Xiaoqian Zhu
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Jiao Li
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Hanping He
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China.
| | - Min Huang
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
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