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Wang H, Zou H, Wang F. Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications. Chembiochem 2024; 25:e202400266. [PMID: 38801028 DOI: 10.1002/cbic.202400266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on-demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA-based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.
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Affiliation(s)
- Hong Wang
- Biological Products Laboratory, Chongqing Institute for Food and Drug Control, Chongqing, 430072, P. R. China
| | - Hanyan Zou
- Biological Products Laboratory, Chongqing Institute for Food and Drug Control, Chongqing, 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
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HE XQ, LUO L, GUO L, XIE JW. An Aptameric Biolayer Interferometric Assay for Detection of Recombinant Human Erythropoietin-α. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ziu I, Laryea ET, Alashkar F, Wu CG, Martic S. A dip-and-read optical aptasensor for detection of tau protein. Anal Bioanal Chem 2020; 412:1193-1201. [PMID: 31900535 DOI: 10.1007/s00216-019-02350-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022]
Abstract
Neurodegeneration currently remains without a differential diagnosis or cure. Tau protein is one of the biomarkers of neurodegenerative diseases commonly known as tauopathies. Tau protein plays an integral role in stabilizing microtubules and cell structure; however, due to post-translational modifications, tau protein undergoes self-assembly into cytotoxic structures and is co-localized intra- and extracellularly. Hence, tau protein is a viable biomarker associated with protein pathogenesis and neurodegeneration. The novel optical biosensor for tau441 protein is based on the aptamer recognition probe and the biolayer interferometry (BLI) method for detection. The current biotin-aptasensor in combination with the streptavidin surface provides real-time monitoring of tau441 protein in the nanomolar range, with the limit of detection at 6.7 nM in vitro. The tau441 detection is achieved with high selectivity over other neurodegeneration biomarkers which include amyloid-β and α-synuclein. The aptasensor also allows for tau441 protein detection in a complex matrix such as fetal bovine serum, indicating its utility in other biological fluids for diagnostic applications. The optical method is simple, rapid and highly selective for point-of-care application which is critical for achieving the early and differential diagnosis of neurodegenerative diseases and identifying their treatments. Graphical abstract.
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Affiliation(s)
- Iva Ziu
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Erving T Laryea
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Fayza Alashkar
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Colin G Wu
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Sanela Martic
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, ON, K9L 0G2, Canada.
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Ouyang S, Hu B, Zhou R, Liu D, Peng D, Li Z, Li Z, Jiao B, Wang L. Rapid and sensitive detection of nodularin-R in water by a label-free BLI aptasensor. Analyst 2019; 143:4316-4322. [PMID: 30101954 DOI: 10.1039/c8an00567b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Contamination of freshwater with nodularin-R (NOD-R) represents a significant global environmental and public health concern. However, ethical problems and technical difficulties surrounding the current detection methods for NOD-R necessitate further studies to devise appropriate alternatives within a regulatory monitoring regime. In this work, we employed an aptamer as a specific recognition element and developed a biolayer interferometry (BLI) biosensor platform for NOD-R detection. The aptasensor we propose displayed a broad detection range from 40 to 600 nM NOD-R (and a linear response range from 40 to 200 nM), and achieved a detection limit as low as 167 pM. In addition, the aptamer-based biosensor was shown to possess high selectivity, as well as good reproducibility and stability. We believe that this novel aptamer-based biosensor provides a potential alternative for the sensitive and rapid detection of NOD-R.
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Affiliation(s)
- Shengqun Ouyang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China.
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Xue SF, Han XY, Chen ZH, Yan Q, Lin ZY, Zhang M, Shi G. The Chemistry of Europium(III) Encountering DNA: Sprouting Unique Sequence-Dependent Performances for Multifunctional Time-Resolved Luminescent Assays. Anal Chem 2018; 90:10614-10620. [PMID: 30099873 DOI: 10.1021/acs.analchem.8b03010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Screening functional DNA that can fruitfully interact with metal ions is a long-standing hot topic in the fields of biotechnology, medicine, and DNA-based sensors. In this paper, we focus on the chemistry of europium(III) (Eu) coupled with single-stranded DNA (ssDNA), and we innovatively unveil that cytosine- and thymine-rich ssDNA oligomers (e.g., C16 and T16) can be effective antenna ligands to sensitize the luminescence of Eu. Luminescence lifetime spectroscopy, circular dichroic (CD) spectroscopy, and isothermal titration calorimetry (ITC) have been used to systematically characterize the interaction involved between Eu and ssDNA. In light of the resultant sequence-dependent performances, the long luminescence lifetime Eu/ssDNA-based label-free and versatile probes are further devised as a pattern distinction system for time-resolved luminescent (TRL) sensing applications. The interactions of metal ions and ssDNA can distinctively shift the antenna effect of ssDNA toward Eu as accessible pattern signals. As a result, as few as two Eu/ssDNA label-free TRL probes can discriminate 17 metal ions via principal component analysis (PCA). In addition, thiols can readily capture metal ions to switch the luminescence of Eu/ssDNA probes initially altered by metal ions. Hence, four Eu/ssDNA-metal ion ensembles are demonstrated to be a powerful label-free TRL sensor array for pattern differentiation of eight thiols and even chiral recognition of cysteine enantiomers with different concentrations. Moreover, the sensitive TRL detection of thiols in biofluids can be successfully realized by using our method, promising its potential practical usage. This is the first report of a ssDNA-sensitized Eu-based TRL platform for label-free yet multifunctional background-free sensing and would open a door for sprouting of more novel lanthanide ion/DNA-relevant strategies toward widespread applications.
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Affiliation(s)
- Shi-Fan Xue
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Xin-Yue Han
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Zi-Han Chen
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Qing Yan
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Zi-Yang Lin
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
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Abstract
Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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GelRed/[G3T]5/Tb3+ hybrid: A novel label-free ratiometric fluorescent probe for H2O2 and oxidase-based visual biosensing. Biosens Bioelectron 2018; 100:526-532. [DOI: 10.1016/j.bios.2017.09.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/26/2017] [Accepted: 09/26/2017] [Indexed: 11/18/2022]
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Gao S, Zheng X, Wu J. A biolayer interferometry-based enzyme-linked aptamer sorbent assay for real-time and highly sensitive detection of PDGF-BB. Biosens Bioelectron 2017; 102:57-62. [PMID: 29125972 DOI: 10.1016/j.bios.2017.11.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/19/2017] [Accepted: 11/02/2017] [Indexed: 02/02/2023]
Abstract
Accurate, fast and sensitive detection of disease-specific protein biomarkers, especially in blood, urine, or other bodily fluids, is an important approach to achieve early disease diagnosis. Platelet-derived growth factor-BB (PDGF-BB), a widely used biomarker, is involved in a substantial number of serious diseases, such as hepatic fibrosis, atherosclerosis, age-related macular degeneration and diabetic eye disease and is often over-expressed in human malignant tumors. Therefore, the development of sensitive and specific detection methods for PDGF-BB is of great importance for the early diagnosis of disease and assessments of patient recovery. In the current study, a biolayer interferometry-based enzyme-linked aptamer sorbent assay (BLI-ELASA) was successfully established for rapid (20-25min), high-throughput (8 or 16 samples) and real-time monitoring of PDGF-BB in clinical samples. The method exhibited a broad detection range from 0.5 to 1000ng/mL of PDGF-BB (good linear range from 0.5 to 10ng/mL), with a low detection limit of 0.08ng/mL. Moreover, BLI-ELASA was applied to the detection of PDGF-BB in spiked serum and urine samples and showed a high degree of selectivity for PDGF-BB, good reproducibility, and stability. We believe that the methodology in this work can be easily adapted to detect other biomolecules in clinical samples, including viruses, pathogens and toxins, in a rapid, sensitive, high-throughput and real-time manner.
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Affiliation(s)
- Shunxiang Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China; Key Laboratory of Myopia, Ministry of Health, Shanghai, China
| | - Xin Zheng
- Department of Laboratory Diagnosis, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jihong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China; Key Laboratory of Myopia, Ministry of Health, Shanghai, China.
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Li D, Cheng W, Li Y, Xu Y, Li X, Yin Y, Ju H, Ding S. Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs. Anal Chem 2016; 88:7500-6. [PMID: 27367785 DOI: 10.1021/acs.analchem.5b04844] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A target-switched DNA nanotweezer is designed for AND logic gate operation and enzyme-free detection of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent DNAzyme formation. The double crossover motif-based nanotweezer consists of an arched structure as the set strand for target inputs and two split G-rich DNAs at the termini of two arms for signal output. Upon a CHA, a small amount of binary target inputs can switch numerous open nanotweezers to a closed state, which leads to the formation of proximity-dependent DNAzyme in the presence of hemin to produce a highly sensitive biosensing system. The binary target inputs can be used for successful building of AND logic gate, which is validated by polyacrylamide gel electrophoresis, surface plasmon resonance and the biosensing signal. The developed biosensing system shows a linear response of the output chemiluminescence signal to input binary miRNAs with a detection limit of 30 fM. It can be used for miRNAs analysis in complex sample matrix. This system provides a simple and reusable platform for logic gate operation and enzyme-free, highly sensitive, and specific multianalysis of miRNAs.
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Affiliation(s)
- Dandan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China.,The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Yujian Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - YongJie Xu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Yibing Yin
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China.,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University , Nanjing 210023, People's Republic of China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
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Dong S, Zhao R, Zhu J, Lu X, Li Y, Qiu S, Jia L, Jiao X, Song S, Fan C, Hao R, Song H. Electrochemical DNA Biosensor Based on a Tetrahedral Nanostructure Probe for the Detection of Avian Influenza A (H7N9) Virus. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8834-42. [PMID: 25844798 DOI: 10.1021/acsami.5b01438] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A DNA tetrahedral nanostructure-based electrochemical biosensor was developed to detect avian influenza A (H7N9) virus through recognizing a fragment of the hemagglutinin gene sequence. The DNA tetrahedral probe was immobilized onto a gold electrode surface based on self-assembly between three thiolated nucleotide sequences and a longer nucleotide sequence containing complementary DNA to hybridize with the target single-stranded (ss)DNA. The captured target sequence was hybridized with a biotinylated-ssDNA oligonucleotide as a detection probe, and then avidin-horseradish peroxidase was introduced to produce an amperometric signal through the interaction with 3,3',5,5'-tetramethylbenzidine substrate. The target ssDNA was obtained by asymmetric polymerase chain reaction (PCR) of the cDNA template, reversely transcribed from the viral lysate of influenza A (H7N9) virus in throat swabs. The results showed that this electrochemical biosensor could specifically recognize the target DNA fragment of influenza A (H7N9) virus from other types of influenza viruses, such as influenza A (H1N1) and (H3N2) viruses, and even from single-base mismatches of oligonucleotides. Its detection limit could reach a magnitude of 100 fM for target nucleotide sequences. Moreover, the cycle number of the asymmetric PCR could be reduced below three with the electrochemical biosensor still distinguishing the target sequence from the negative control. To the best of our knowledge, this is the first report of the detection of target DNA from clinical samples using a tetrahedral DNA probe functionalized electrochemical biosensor. It displays that the DNA tetrahedra has a great potential application as a probe of the electrochemical biosensor to detect avian influenza A (H7N9) virus and other pathogens at the gene level, which will potentially aid the prevention and control of the disease caused by such pathogens.
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Affiliation(s)
- Shibiao Dong
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
- ‡Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China
| | - Rongtao Zhao
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Jiangong Zhu
- ∥Clinical Diagnostic Center, 302 Hospital of PLA, Beijing 100039, China
| | - Xiao Lu
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yang Li
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Shaofu Qiu
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Leili Jia
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiong Jiao
- ‡Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China
| | - Shiping Song
- §Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- §Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - RongZhang Hao
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - HongBin Song
- †Institute for Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
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Auld D, Lea W, Davis MI, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2013; 11:139-51. [DOI: 10.1089/adt.2013.1103.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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