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Dekaliuk M, Farka Z, Hildebrandt N. The pros and cons of nucleic acid-amplified immunoassays-a comparative study on the quantitation of prostate-specific antigen with and without rolling circle amplification. Anal Bioanal Chem 2024:10.1007/s00216-024-05357-y. [PMID: 38849527 DOI: 10.1007/s00216-024-05357-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024]
Abstract
Integrating isothermal nucleic acid amplification strategies into immunoassays can significantly decrease analytical limits of detection (LODs). On the other hand, an amplification step adds time, complication, reagents, and costs to the assay format. To evaluate the pros and cons in the context of heterogeneous multistep immunoassays, we quantified prostate-specific antigen (PSA) with and without rolling circle amplification (RCA). In addition, we compared time-gated (TG) with continuous-wave (CW) photoluminescence (PL) detection using a terbium complex and a fluorescein dye, respectively. For both direct (non-amplified) and amplified assays, TG PL detection provided circa four- to eightfold lower LODs, illustrating the importance of autofluorescence background suppression even for multi-wash assay formats. Amplified assays required an approximately 2.4 h longer assay time but led to almost 100-fold lower LODs down to 1.3 pg/mL of PSA. Implementation of TG-FRET (using a Tb-Cy5.5 donor-acceptor pair) into the RCA immunoassay resulted in a slightly higher LOD (3.0 pg/mL), but the ratiometric detection format provided important benefits, such as higher reproducibility, lower standard deviations, and multiplexing capability. Overall, our direct comparison demonstrated the importance of biological background suppression even in heterogeneous assays and the potential of using isothermal RCA for strongly decreasing analytical LODs, making such assays viable alternatives to conventional enzyme-linked immunosorbent assays (ELISAs).
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Affiliation(s)
- Mariia Dekaliuk
- Laboratory of Molecular Assays and Imaging, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznań, Poland.
- Laboratoire COBRA, CNRS, INSA Rouen, Université de Rouen Normandie, Normandie Université, Rouen, France.
| | - Zdeněk Farka
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Niko Hildebrandt
- Laboratoire COBRA, CNRS, INSA Rouen, Université de Rouen Normandie, Normandie Université, Rouen, France.
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, L8S 4L7, Canada.
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2
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Wang M, Liu Z, Liu C, He W, Qin D, You M. DNAzyme-based ultrasensitive immunoassay: Recent advances and emerging trends. Biosens Bioelectron 2024; 251:116122. [PMID: 38382271 DOI: 10.1016/j.bios.2024.116122] [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: 10/18/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Immunoassay, as the most commonly used method for protein detection, is simple to operate and highly specific. Sensitivity improvement is always the thrust of immunoassays, especially for the detection of trace quantities. The emergence of artificial enzyme, i.e., DNAzyme, provides a novel approach to improve the detection sensitivity of immunoassay. Simultaneously, its advantages of simple synthesis and high stability enable low cost, broad applicability and long shelf life for immunoassay. In this review, we summarized the recent advances in DNAzyme-based immunoassay. First, we summarized the existing different DNAzymes based on their catalytic activities. Next, the common signal amplification strategies used for DNAzyme-based immunoassays were reviewed to cater to diverse detection requirements. Following, the wide applications in disease diagnosis, environmental monitoring and food safety were discussed. Finally, the current challenges and perspectives on the future development of DNAzyme-based immunoassays were also provided.
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Affiliation(s)
- Meng Wang
- Department of Biomedical Engineering, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Zhe Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China; Department of Rehabilitation Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, PR China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Wanghong He
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China; Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, PR China
| | - Dui Qin
- Department of Biomedical Engineering, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China.
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China.
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3
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Zhou J, Wang Y, Zhou C, Zheng L, Fu L. A ratiometric fluorescent aptasensor based on EXPAR to detect shellfish tropomyosin in food system. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhou W, Liao L, Fan X, Yao J, Jiang B. Programmable bidirectional dynamic DNA nano-device for accurate and ultrasensitive fluorescent detection of trace MUC1 biomarker in serums. Anal Chim Acta 2022; 1238:340643. [DOI: 10.1016/j.aca.2022.340643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022]
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Lengfeld J, Zhang H, Stoesz S, Murali R, Pass F, Greene MI, Goel PN, Grover P. Challenges in Detection of Serum Oncoprotein: Relevance to Breast Cancer Diagnostics. BREAST CANCER-TARGETS AND THERAPY 2021; 13:575-593. [PMID: 34703307 PMCID: PMC8524259 DOI: 10.2147/bctt.s331844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer is a highly prevalent malignancy that shows improved outcomes with earlier diagnosis. Current screening and monitoring methods have improved survival rates, but the limitations of these approaches have led to the investigation of biomarker evaluation to improve early diagnosis and treatment monitoring. The enzyme-linked immunosorbent assay (ELISA) is a specific and robust technique ideally suited for the quantification of protein biomarkers from blood or its constituents. The continued clinical relevancy of this assay format will require overcoming specific technical challenges, including the ultra-sensitive detection of trace biomarkers and the circumventing of potential assay interference due to the expanding use of monoclonal antibody (mAb) therapeutics. Approaches to increasing the sensitivity of ELISA have been numerous and include employing more sensitive substrates, combining ELISA with the polymerase chain reaction (PCR), and incorporating nanoparticles as shuttles for detection antibodies and enzymes. These modifications have resulted in substantial boosts in the ability to detect extremely low levels of protein biomarkers, with some systems reliably detecting antigen at sub-femtomolar concentrations. Extensive utilization of mAb therapies in oncology has presented an additional contemporary challenge for ELISA, particularly when both therapeutic and assay antibodies target the same protein antigen. Resolution of issues such as epitope overlap and steric hindrance requires a rational approach to the design of diagnostic antibodies that takes advantage of modern antibody generation pipelines, epitope binning techniques and computational methods to strategically target biomarker epitopes. This review discusses technical strategies in ELISA implemented to date and their feasibility to address current constraints on sensitivity and problems with interference in the clinical setting. The impact of these recent advancements will depend upon their transformation from research laboratory protocols into facile, reliable detection systems that can ideally be replicated in point-of-care devices to maximize utilization and transform both the diagnostic and therapeutic monitoring landscape.
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Affiliation(s)
- Justin Lengfeld
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Stoesz
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology; Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Franklin Pass
- Martell Diagnostic Laboratories, Inc., Roseville, MN, 55113, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peeyush N Goel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Payal Grover
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Branca M, Calvet C, Limoges B, Mavré F. Specific Versus Non-specific Response in Exponential Molecular Amplification from Cross-Catalysis: Modeling the Influence of Background Amplifications on the Analytical Performances. Chemphyschem 2021; 22:1611-1621. [PMID: 34038617 DOI: 10.1002/cphc.202100342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/25/2021] [Indexed: 11/05/2022]
Abstract
Molecule based signal amplifications relying on an autocatalytic process may represent an ideal strategy for the development of ultrasensitive analytical or bioanalytical assays, the main reason being the exponential nature of the amplification. However, to take full advantage of such amplification rates, high stability of the starting co-reactants is required in order to avoid any undesirable background amplification. Here, on the basis of a simple kinetic model of cross-catalysis including a certain degree of intrinsic instability of co-reactants, we highlight the key parameters governing the analytical response of the system and discuss the analytical performances that are expected from a given kinetic set. In particular, we show how the detection limit is directly related to the relative instability of reactants within each catalytic loop. The model is validated with an experimental dataset and is intended to serve as a guide in the design and optimization of autocatalytic molecular-based amplification systems with improved analytical performances.
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Affiliation(s)
- Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Corentin Calvet
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
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Şahin S, Caglayan MO, Üstündağ Z. Recent advances in aptamer-based sensors for breast cancer diagnosis: special cases for nanomaterial-based VEGF, HER2, and MUC1 aptasensors. Mikrochim Acta 2020; 187:549. [PMID: 32888061 DOI: 10.1007/s00604-020-04526-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023]
Abstract
Cancer is one of the most common and important diseases with a high mortality rate. Breast cancer is among the three most common types of cancer in women, and the mortality rate has reached 0.024% in some countries. For early-stage preclinical diagnosis of breast cancer, sensitive and reliable tools are needed. Today, there are many types of biomarkers that have been identified for cancer diagnosis. A wide variety of detection strategies have also been developed for the detection of these biomarkers from serum or other body fluids at physiological concentrations. Aptamers are single-stranded DNA or RNA oligonucleotides and promising in the production of more sensitive and reliable biosensor platforms in combination with a wide range of nanomaterials. Conformational changes triggered by the target analyte have been successfully applied in fluorometric, colorimetric, plasmonic, and electrochemical-based detection strategies. This review article presents aptasensor approaches used in the detection of vascular endothelial growth factor (VEGF), human epidermal growth factor receptor 2 (HER2), and mucin-1 glycoprotein (MUC1) biomarkers, which are frequently studied in the diagnosis of breast cancer. The focus of this review article is on developments of the last decade for detecting these biomarkers using various sensitivity enhancement techniques and nanomaterials.
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Affiliation(s)
- Samet Şahin
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
| | | | - Zafer Üstündağ
- Department of Chemistry, Kütahya Dumlupınar University, 43100, Kütahya, Turkey
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Wang Y, Zhao X, Zhang M, Sun X, Bai J, Peng Y, Li S, Han D, Ren S, Wang J, Han T, Gao Y, Ning B, Gao Z. A fluorescent amplification strategy for high-sensitive detection of 17 β-estradiol based on EXPAR and HCR. Anal Chim Acta 2020; 1116:1-8. [PMID: 32389184 DOI: 10.1016/j.aca.2020.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
Environmental endocrine disruptors in the environment and food, especially 17 β-estradiol (E2), are important factors affecting the growth and development of organisms. In this research, we constructed a fluorescence strategy for two-step amplification that combined two currently popular methods, exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR). E2 competed with the complementary DNA (cDNA) to bind the aptamer modified on the magnetic beads. The free complementary strand in the supernatant was used as a trigger sequence to activate EXPAR, producing a large amount of short single-stranded DNA (ssDNA). The amplified ssDNA can trigger the second HCR amplification, producing many long double-stranded DNA (dsDNA) analogues. According to the principle of fluorescence resonance energy transfer, the carboxyfluorescein (FAM) signals in H1 and H2 hairpins were quenched by black hole quencher (BHQ-1). After the addition of E2 and initiation of amplification, the initially quenched fluorescent signal would be restored. This strategy with a detection limit of 0.37 pg mL-1 (S/N = 3) showed a good linear relationship in the range of 0.4-800 pg mL-1. In addition, the recovery rates of the method for milk and water samples were 98.55%-116.95% and 92.32%-107.00%, respectively. This is the first report of the combined detection of EXPAR and HCR, providing a reference for rapid and highly sensitive detection using multiple isothermal amplification methods.
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Affiliation(s)
- Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Xudong Zhao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Man Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology. Shanghai, 200093, PR China
| | - Xuan Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Jiang Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Yifei Gao
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Baoan Ning
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China.
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Bodulev OL, Sakharov IY. Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:147-166. [PMID: 32093592 PMCID: PMC7223333 DOI: 10.1134/s0006297920020030] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022]
Abstract
Recently, there has been a rapid progress in the development of techniques for isothermal amplification of nucleic acids as an alternative to polymerase chain reaction (PCR). The advantage of these methods is that the nucleic acids amplification can be carried out at constant temperature, unlike PCR, which requires cyclic temperature changes. Moreover, isothermal amplification can be conducted directly in living cells. This review describes the principles of isothermal amplification techniques and demonstrates their high efficiency in designing new highly sensitive detection methods of nucleic acids and enzymes involved in their modifications. The data on successful application of isothermal amplification methods for the analysis of cells and biomolecules with the use of DNA/RNA aptamers are presented.
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Affiliation(s)
- O L Bodulev
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia
| | - I Yu Sakharov
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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