1
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Cao D, Qin X, Wang W, Zhang Y, Peng S, Gong H, Luo Q, Yang J. Designing a Hybrid Chain Reaction Probe for Multiplex Transcripts Assay with High-Level Imaging. ACS NANO 2024; 18:618-629. [PMID: 38154106 DOI: 10.1021/acsnano.3c08720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
The hybrid chain reaction (HCR), an isothermal and enzyme-free amplification strategy, has found extensive use in fluorescent in situ hybridization (FISH) assays. However, the existing HCRs are limited, being time-consuming processes and low-efficiency imaging due to weak signal, significantly restricting their application in transcriptomic assays. To address the limitations, we developed nine orthogonal HCR hairpin-pair (hp) probes in this study to enable efficient signal amplification for multiplex assays. To enhance the efficiency and imaging quality of multiplex assays using these HCR probes, we employed two strategies. First, we coupled fluorescent molecules to HCR hairpins via disulfide bonds, facilitating easy removal through chemical cleavage. As a result, the workflow was greatly simplified. Second, we combined HCR with in situ rolling circle amplification (ISRCA), creating ISRCA-HCR, which achieved a 17-fold signal amplification. ISRCA-HCR demonstrated a high-level imaging capability for spatial cell type assays. This study shows the application for cell typing based on the developed HCR probes, enabling accurate and high-level signal amplification for multiplex FISH imaging. This provides an effective research tool for transcriptome and spatial cell type analysis.
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Affiliation(s)
- Dongjian Cao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xinxin Qin
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wenjing Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Zhang
- Class 202001, School of Engineering Science, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Sunxiang Peng
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hui Gong
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Qingming Luo
- School of Biomedical Engineering, Hainan University, Haikou 570228, China
| | - Jie Yang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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2
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Nourizad A, Golmohammadi S, Aghanejad A, Tohidkia MR. Recent trends in aptamer-based nanobiosensors for detection of vascular endothelial growth factors (VEGFs) biomarker: A review. ENVIRONMENTAL RESEARCH 2023; 236:116726. [PMID: 37495062 DOI: 10.1016/j.envres.2023.116726] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]
Abstract
Vascular endothelial growth factor (VEGF) is a remarkable cytokine that plays an important role in regulating vascular formation during the angiogenesis process. Therefore, real-time detection and quantification of VEGF is essential for clinical diagnosis and treatment due to its overexpression in various tumors. Among various sensing strategies, the aptamer-based sensors in combination with biological molecules improve the detection ability VEGFs. Aptamers are suitable biological recognition agents for the preparation of sensitive and reproducible aptasensors (Apt-sensors) due to their low immunogenicity, simple and straightforward chemical modification, and high resistance to denaturation. Here, a summary of the strategies for immobilization of aptamers (e.g., direct or self-assembled monolayer (SAM) attachment, etc.) on different types of electrodes was provided. Moreover, we discussed nanoparticle deposition techniques and surface modification methods used for signal amplification in the detection of VEGF. Furthermore, we are investigating various types of optical and electrochemical Apt-sensors used to improve sensor characterization in the detection of VEGF biomarkers.
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Affiliation(s)
- Abolfazl Nourizad
- Research Center for Pharmaceutical Nanotechnology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Electronics, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Saeed Golmohammadi
- Department of Electronics, Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Ayuob Aghanejad
- Research Center for Pharmaceutical Nanotechnology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Nuclear Medicine, Faculty of Medicine, Imam Reza General Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Reza Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Chen W, Liu F, Zhang C, Duan Y, Ma J, Wang Y, Chen G. A review of advances in aptamer-based cell detection technology. Mol Biol Rep 2023; 50:5425-5438. [PMID: 37101007 DOI: 10.1007/s11033-023-08410-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/24/2023] [Indexed: 04/28/2023]
Abstract
Since cells are the basic structural and functional units of organisms, the detection or quantitation of cells is one of the most common basic problems in life science research. The established cell detection techniques mainly include fluorescent dye labeling, colorimetric assay, and lateral flow assay, all of which employ antibodies as cell recognition elements. However, the widespread application of the established methods generally dependent on antibodies is limited, because the preparation of antibodies is complicated and time-consuming, and unrecoverable denaturation is prone to occur with antibodies. By contrast, aptamers that are generally selected through the systematic evolution of ligands by exponential enrichment can avoid the disadvantages of antibodies due to their controllable synthesis, thermostability, and long shelf life, etc. Accordingly, aptamers may serve as novel molecular recognition elements like antibodies in combination with various techniques for cell detection. This paper reviews the developed aptamer-based cell detection methods, mainly including aptamer-fluorescent labeling, aptamer-isothermal amplification assay, electrochemical aptamer sensor, aptamer-based lateral flow analysis, and aptamer-colorimetric assay. The principles, advantages, progress of application in cell detection and future development trend of these methods were specially discussed. Overall, different assays are suitable for different detection purposes, and the development of more accurate, economical, efficient, and rapid aptamer-based cell detection methods is always on the road in the future. This review is expected to provide a reference for achieving efficient and accurate detection of cells as well as improving the usefulness of aptamers in the field of analytical applications.
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Affiliation(s)
- Wenrong Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China.
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Jinju Ma
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China.
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4
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Xia X, Zhang G, Pica Ciamarra M, Jiao Y, Ni R. The Role of Receptor Uniformity in Multivalent Binding. JACS AU 2023; 3:1385-1391. [PMID: 37234107 PMCID: PMC10207130 DOI: 10.1021/jacsau.3c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the selectivity in multivalent targeting. Here, using analytical mean field theory and Monte Carlo simulations, we discover that, for receptors that are highly uniformly distributed, the highest selectivity occurs at an intermediate binding energy and can be significantly greater than the weak binding limit. This is caused by an exponential relationship between the bound fraction and receptor concentration, which is influenced by both the strength and combinatorial entropy of binding. Our findings not only provide new guidelines for the rational design of biosensors using multivalent nanoparticles but also introduce a new perspective in understanding biological processes involving multivalency.
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Affiliation(s)
- Xiuyang Xia
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
- Division
of Physics and Applied Physics, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Ge Zhang
- Department
of Physics, City University of Hong Kong, 518057 Kowloon, Hong Kong China
| | - Massimo Pica Ciamarra
- Division
of Physics and Applied Physics, School of Physical and Mathematical
Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Yang Jiao
- Materials
Science and Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Ran Ni
- School
of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore
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5
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Ma Z, Wang J, Lu X, Zhou G, Wu Y, Zhang D, Li L, Guo L. A dual-blocker aided and dual-label-free electrochemical biosensor based on mbHCR/rGO nanocomplexes for ultrasensitive DNA detection. Talanta 2023; 260:124646. [PMID: 37187028 DOI: 10.1016/j.talanta.2023.124646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/10/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023]
Abstract
Heterogeneous electrochemical DNA biosensors have attracted huge attention due to their enhanced signal sensitivity, compared to homogeneous biosensors. However, the high cost of probe labeling and the reduced recognition efficiency associated with current heterogeneous electrochemical biosensors confine their potential applications. In the present work, a dual-blocker assisted and dual-label-free heterogeneous electrochemical strategy based on multi-branched hybridization chain reaction (mbHCR) and reduced graphene oxide (rGO) was fabricated for ultrasensitive detection of DNA. The target DNA could trigger the mbHCR of two DNA hairpin probes, resulting in the generation of multi-branched long chain of DNA duplexes with bidirectional arms. One direction of the multi-branched arms in the mbHCR products were then bound to the label-free capture probe on the gold electrode through multivalent hybridization with enhanced recognition efficiency. The other direction of multi-branched arms in mbHCR product could adsorb rGO via π-π stacking interactions. Two DNA blockers were ingeniously designed to block the binding of excessive H1-pAT on electrode and to prevent the adsorption of rGO by residual unbound capture probes. As a result, with the electrochemical reporter methylene blue selectively intercalated into the long chain of DNA duplex and absorbed on rGO, a remarkable electrochemical signal rise was observed. Thus, a dual-blocker aided and dual-label-free electrochemical strategy for ultrasensitive DNA detection is readily realized with the merit of cost-effective. The as-developed dual-label-free electrochemical biosensor has great potential to be employed in nucleic acid related medical diagnostics.
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Affiliation(s)
- Zeyu Ma
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China
| | - Jingyu Wang
- Department of Pathology, First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, 314000, PR China
| | - Xing Lu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China
| | - Guobao Zhou
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China.
| | - Yi Wu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China
| | - Dan Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China
| | - Lei Li
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China.
| | - Longhua Guo
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, PR China; Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, 314001, PR China
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6
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A nucleolin-activated polyvalent aptamer nanoprobe for the detection of cancer cells. Anal Bioanal Chem 2023; 415:2217-2226. [PMID: 36864310 DOI: 10.1007/s00216-023-04629-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Sensitive detection of cancer cells plays a critical role in early cancer diagnosis. Nucleolin, overexpressed on the surface of cancer cells, is regarded as a candidate biomarker for cancer diagnosis. Thus, cancer cells can be detected through the detection of membrane nucleolin. Herein, we designed a nucleolin-activated polyvalent aptamer nanoprobe (PAN) to detect cancer cells. In brief, a long single-stranded DNA with many repeated sequences was synthesized through rolling circle amplification (RCA). Then the RCA product acted as a scaffold chain to combine with multiple AS1411 sequences, which was doubly modified with fluorophore and quenching group, respectively. The fluorescence of PAN was initially quenched. Upon binding to target protein, the conformation of PAN changed, leading to the recovery of fluorescence. The fluorescence signal of cancer cells treated with PAN was much brighter compared with that of monovalent aptamer nanoprobes (MAN) at the same concentration. Furthermore, the binding affinity of PAN to B16 cells was proved to be 30 times higher than that of MAN by calculating the dissociation constants. The results indicated that PAN could specifically detect target cells, and this design concept has potential to become promising in cancer diagnosis.
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7
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Cao X, Chen C, Zhu Q. Biosensors based on functional nucleic acids and isothermal amplification techniques. Talanta 2023; 253:123977. [PMID: 36201957 DOI: 10.1016/j.talanta.2022.123977] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.
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Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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8
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Lee J, Suh HN, Park HB, Park YM, Kim HJ, Kim S. Regenerative Strategy of Gold Electrodes for Long-Term Reuse of Electrochemical Biosensors. ACS OMEGA 2023; 8:1389-1400. [PMID: 36643538 PMCID: PMC9835648 DOI: 10.1021/acsomega.2c06851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Gold is of considerable interest for electrochemical active surfaces because thiol-modified chemicals and biomolecules can be easily immobilized with a simple procedure. However, most gold surfaces are damaged with repetitive measurements, so they are difficult to reuse. Here we demonstrate a novel electrochemical cleaning method of gold surfaces to reuse electrodes with a simple protocol that is easy and nontoxic. This electrochemical cleaning consists of two steps by using different solutions. The 1st step is a cyclic voltammetry sweep using a very low concentration of sulfuric acid, and the 2nd step is a cyclic voltammetry sweep using potassium ferricyanide. Different cleaning methods were also considered for comparison. Consequently, after assembling and desorption of the cell and antigen, the changes in gold electrode performance, as immunosensor and cytosensor, were investigated by electrochemical impedance and cyclic voltammetry. It was found that repetitive measurement is possible until five times while maintaining the reproducibility. It is believed that this method is capable of enabling reuse of gold electrodes and can be used for long-term and accurate monitoring of biological effects, especially at a low cost.
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Affiliation(s)
- JuKyung Lee
- Department
of Medical IT Convergence, Kumoh National
Institute of Technology, Gumi, Gyeongbuk39177, Korea
| | - Han Na Suh
- Korea
Institute of Toxicology, Jeongeup, Jeollabuk-do56212, Korea
| | - Hye-bin Park
- Digital
Health Care Research Center, Gumi Electronics
and Information Technology Research Institute (GERI), Gumi, Gyeongbuk39253, Korea
| | - Yoo Min Park
- Division
of Nano-Bio sensors/Chips development, National
NanoFab Center, Daejeon34141, Korea
| | - Hyung Jin Kim
- Digital
Health Care Research Center, Gumi Electronics
and Information Technology Research Institute (GERI), Gumi, Gyeongbuk39253, Korea
| | - SangHee Kim
- Department
of Medical IT Convergence, Kumoh National
Institute of Technology, Gumi, Gyeongbuk39177, Korea
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9
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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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10
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Xu Y, Zhang T, Li Z, Liu X, Zhu Y, Zhao W, Chen H, Xu J. Photoelectrochemical Cytosensors. ELECTROANAL 2022. [DOI: 10.1002/elan.202100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yi‐Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Tian‐Yang Zhang
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Zheng Li
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Xiang‐Nan Liu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Yuan‐Cheng Zhu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
- State Key Laboratory of Pharmaceutical Biotechnology School of Life Science Nanjing University Nanjing 210023 China
| | - Wei‐Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Jing‐Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
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11
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Wu Q, Liu C, Liu Y, Cui C, Ge J, Tan W. Multibranched Linear DNA-Controlled Assembly of Silver Nanoclusters and Their Applications in Aptamer-Based Cell Recognition. ACS APPLIED MATERIALS & INTERFACES 2022; 14:14953-14960. [PMID: 35344322 DOI: 10.1021/acsami.1c24547] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA-templated silver nanoclusters (DNA-AgNCs) are promising fluorescent materials and have been used in cancer diagnosis. Although many different DNA-AgNC applications have been realized, most of them rely on individual DNA-AgNCs or assembled DNA-AgNCs with limited recognition abilities, resulting in low detection sensitivity or off-target effects, in turn, hindering the performance of DNA-AgNCs in cancer cell recognition. As a solution, we assembled DNA-AgNCs by a multibranched linear (MBL) DNA structure formed through a trigger-initiated hybridization chain reaction (HCR) regarding the natural compatibility of DNA-AgNCs with DNA programmability and the advantages of DNA assembly in incorporating repetitive and functional moieties into one structure. By the specific modification of the trigger, MBL-AgNCs tethered with the targeting aptamer and partially hybridized duplex, which works as a component of DNA logic platform relying on the combination of cascade strand displacement reaction and specific recognition ability of aptamers, were obtained, respectively. DNA-AgNCs assembled by the aptamer-tethered MBL structure exhibited about 20-fold enhanced detection sensitivity in recognizing cancer cells compared to individual aptamer-tethered DNA-AgNCs. DNA-AgNCs assembled by the duplex-attached MBL exhibited logic performance in analyzing dual cell surface receptors with the assistance of "AND" logic platform, thus identifying cancer cells with high sensitivity and resolution. The facile conjugation of the MBL structure with different functional DNA structures makes it an ideal platform to assemble DNA-AgNCs used for aptamer-based cell recognition, thus broadening the potential applications of DNA-AgNCs.
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Affiliation(s)
- Qiong Wu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Chengcheng Liu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yuan Liu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Jia Ge
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Weihong Tan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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12
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Shi J, Zhao C, Shen M, Chen Z, Liu J, Zhang S, Zhang Z. Combination of microfluidic chips and biosensing for the enrichment of circulating tumor cells. Biosens Bioelectron 2022; 202:114025. [DOI: 10.1016/j.bios.2022.114025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
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13
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Liu S, Liu Z, Wang H, Wang J, Liu R, Wang K, Huang J. A novel FRET-based dendritic hybridization chain reaction for tumour-related mRNA imaging. Chem Commun (Camb) 2022; 58:1414-1417. [PMID: 34994763 DOI: 10.1039/d1cc06009k] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel FRET-based dendritic hybridization chain reaction (D-HCR) for TK1 mRNA imaging in living cells was developed. Compared with traditional complex D-HCR methods, it includes the advantages of having a simple design, an accurate signal and is suitable for use with living cells.
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Affiliation(s)
- Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
| | - Zhenxiang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
| | - Huimin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
| | - Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
| | - Ruiting Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China.
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14
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Zhang B, Tian T, Xiao D, Gao S, Cai X, Lin Y. Facilitating In Situ Tumor Imaging with a Tetrahedral DNA Framework‐Enhanced Hybridization Chain Reaction Probe. ADVANCED FUNCTIONAL MATERIALS 2022. [DOI: 10.1002/adfm.202109728] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Bowen Zhang
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Sichuan Chengdu 610041 China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Sichuan Chengdu 610041 China
| | - Dexuan Xiao
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Sichuan Chengdu 610041 China
| | - Shaojingya Gao
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Sichuan Chengdu 610041 China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Sichuan Chengdu 610041 China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Sichuan Chengdu 610041 China
- College of Biomedical Engineering Sichuan University Sichuan Chengdu 610041 China
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15
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Peng Y, Lu B, Deng Y, Yang N, Li G. A dual-recognition-controlled electrochemical biosensor for accurate and sensitive detection of specific circulating tumor cells. Biosens Bioelectron 2022; 201:113973. [PMID: 35021133 DOI: 10.1016/j.bios.2022.113973] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 12/22/2022]
Abstract
Accurate and sensitive assay of specific circulating tumor cells (CTCs) is of importance for the diagnosis, treatment, and metastasis monitoring of cancer. Herein, we have proposed a dual-recognition-controlled electrochemical biosensor in this work for the detection of specific CTCs. To this sensor, two aptamer hairpin probes are designed to be able to separately bind to two adjacent proteins on the cell membrane to activate the associative toehold for strand displacement reaction, which will then trigger a dimer-like rolling cycle amplification reaction, and finally produce significantly amplified electrochemical signals for sensitive quantification of target CTCs. In our design, only the case that the two proteins are simultaneously expressed on the cell membrane can result in obvious signal responses, which may greatly improve the accuracy of CTCs analysis. The proposed biosensor can possess excellent selectivity to distinguish target cells from different cancer cells. Moreover, the combination of rolling cycle amplification and DNA nanostructure capture probes can effectively lower the detection limit to 3 cells mL-1. Notably, our biosensor can be applied to the assay of the target CTCs in the complex whole blood matrixes, verifying its strong stability and anti-interference. Thus, the as-proposed dual-recognition-controlled electrochemical biosensor may exhibit great promise in clinical cancer diagnosis and personalized medicine.
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Affiliation(s)
- Ying Peng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Bing Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Ying Deng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Nana Yang
- Department of Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
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16
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Zhang J, Huang Y, Sun M, Wan S, Yang C, Song Y. Recent Advances in Aptamer-Based Liquid Biopsy. ACS APPLIED BIO MATERIALS 2022; 5:1954-1979. [PMID: 35014838 DOI: 10.1021/acsabm.1c01202] [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] [Indexed: 02/08/2023]
Abstract
Liquid biopsy capable of noninvasive and real-time molecular profiling is considered as a breakthrough technology, endowing an opportunity for precise diagnosis of individual patients. Extracellular vesicles (EVs) and circulating tumor cells (CTCs) consisting of substantial disease-related molecular information play an important role in liquid biopsy. Therefore, it is critically significant to exploit high-performance recognition ligands for efficient isolation and analysis of EVs and CTCs from complex body fluids. Aptamers exhibit extraordinary merits of high specificity and affinity, which are considered as superior recognition ligands for liquid biopsy. In this review, we first summarize recent advanced strategies for the evolution of high-performance aptamers and the construction of various aptamer-based recognition elements. Subsequently, we mainly discuss the isolation and analysis of EVs and CTCs based on the aptamer functioned biomaterials/biointerface. Ultimately, we envision major challenges and future direction of aptamer-based liquid biopsy for clinical utilities.
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Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Miao Sun
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shuang Wan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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17
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Yao C, Zhu C, Tang J, Ou J, Zhang R, Yang D. T Lymphocyte-Captured DNA Network for Localized Immunotherapy. J Am Chem Soc 2021; 143:19330-19340. [PMID: 34780151 DOI: 10.1021/jacs.1c07036] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The efficient isolation of immune cells with high purity and low cell damage is important for immunotherapy and remains highly challenging. We herein report a cell capture DNA network containing polyvalent multimodules for the specific isolation and in situ incubation of T lymphocytes (T-cells). Two ultralong DNA chains synthesized by an enzymatic amplification process were rationally designed to include functional multimodules as cell anchors and immune adjuvants. Mutually complementary sequences facilitated the formation of a DNA network and encapsulation of T-cells, as well as offering cutting sites of a restriction enzyme for the responsive release of T-cells and immune adjuvants. The purity of captured tumor-infiltrating T-cells reached 98%, and the viability of T-cells maintained ∼90%. The T-cells-containing DNA network was further administrated to a tumor lesion for localized immunotherapy. Our work provides a robust nanobiotechnology for efficient isolation of immune cells and other biological particles.
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Affiliation(s)
- Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Chenxu Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jianpu Tang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Junhan Ou
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Rui Zhang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
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18
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Wang C, Xu Y, Zhao X, Li S, Qian Q, Wang W, Mi X. A double-tetrahedral DNA framework based electrochemical biosensor for ultrasensitive detection and release of circulating tumor cells. Analyst 2021; 146:6474-6481. [PMID: 34585683 DOI: 10.1039/d1an01470f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Detecting circulating tumor cells (CTCs) in patients' blood is essential for early diagnosis, precise treatment and prognosis of cancer. Yet due to CTCs being extremely rare in the peripheral blood of patients, it is still a challenge to detect CTCs with high sensitivity and high selectivity. Here, we developed a double-tetrahedral DNA framework (DTDF) based electrochemical biosensor system (E-CTC sensor system) for ultrasensitive detection and release of CTCs. In this work, an upright tetrahedral DNA framework (UTDF) was used as a rigid scaffold to modify a screen-printed gold electrode (SPGE), and an inverted tetrahedral DNA framework (ITDF) provided three vertex chains to multivalently bind with aptamers. Meanwhile, a streptavidin tagged horseradish peroxidase homopolymer (SA-polyHRP) was linked to biotin-modified aptamers to significantly amplify the signal. Moreover, the captured CTCs could be effectively released via benzonase nuclease with little cell damage. Our E-CTC sensor system achieved a linear range from 1 to 105 MCF-7 cells with an ultralow detection limit of 1 cell. The release efficiency reached 88.1%-97.6% and the viability of the released cells reached up to 98%. We also detected the MCF-7 cells in mimic whole blood samples, suggesting that the E-CTC sensor system shows promise for use in clinical research.
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Affiliation(s)
- Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Xu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiaoshuang Zhao
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
| | - Shuainai Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Shanghai Pudong New District Zhoupu Hospital (Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital), Shanghai 201318, China.
| | - Xianqiang Mi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China. .,CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai 200050, China.,Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 310024 Hangzhou, China
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19
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Rhouati A, Marty JL, Vasilescu A. Electrochemical biosensors combining aptamers and enzymatic activity: Challenges and analytical opportunities. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Recent Development of Nanomaterials-Based Cytosensors for the Detection of Circulating Tumor Cells. BIOSENSORS-BASEL 2021; 11:bios11080281. [PMID: 34436082 PMCID: PMC8391755 DOI: 10.3390/bios11080281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022]
Abstract
The accurate analysis of circulating tumor cells (CTCs) holds great promise in early diagnosis and prognosis of cancers. However, the extremely low abundance of CTCs in peripheral blood samples limits the practical utility of the traditional methods for CTCs detection. Thus, novel and powerful strategies have been proposed for sensitive detection of CTCs. In particular, nanomaterials with exceptional physical and chemical properties have been used to fabricate cytosensors for amplifying the signal and enhancing the sensitivity. In this review, we summarize the recent development of nanomaterials-based optical and electrochemical analytical techniques for CTCs detection, including fluorescence, colorimetry, surface-enhanced Raman scattering, chemiluminescence, electrochemistry, electrochemiluminescence, photoelectrochemistry and so on.
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21
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Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
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Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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22
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Hui X, Yang C, Li D, He X, Huang H, Zhou H, Chen M, Lee C, Mu X. Infrared Plasmonic Biosensor with Tetrahedral DNA Nanostructure as Carriers for Label-Free and Ultrasensitive Detection of miR-155. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100583. [PMID: 34155822 PMCID: PMC8373097 DOI: 10.1002/advs.202100583] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/19/2021] [Indexed: 05/27/2023]
Abstract
MicroRNAs play an important role in early development, cell proliferation, apoptosis, and cell death, and are aberrantly expressed in many types of cancers. To understand their function and diagnose cancer at an early stage, it is crucial to quantitatively detect microRNA without invasive labels. Here, a plasmonic biosensor based on surface-enhanced infrared absorption (SEIRA) for rapid, label-free, and ultrasensitive detection of miR-155 is reported. This technology leverages metamaterial perfect absorbers stimulating the SEIRA effect to provide up to 1000-fold near-field intensity enhancement over the microRNA fingerprint spectral bands. Additionally, it is discovered that the limit of detection (LOD) of the biosensor can be greatly improved by using tetrahedral DNA nanostructure (TDN) as carriers. By using near-field enhancement of SEIRA and specific binding of TDN, the biosensor achieves label-free detection of miR-155 with a high sensitivity of 1.162% pm-1 and an excellent LOD of 100 × 10-15 m. The LOD is about 5000 times lower than that using DNA single strand as probes and about 100 times lower than that of the fluorescence detection method. This work can not only provide a powerful diagnosis tool for the microRNAs detection but also gain new insights into the field of label-free and ultrasensitive SEIRA-based biosensing.
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Affiliation(s)
- Xindan Hui
- Key Laboratory of Optoelectronic Technology and SystemsMinistry of EducationInternational R&D Center of Micro‐Nano Systems and New Materials TechnologyChongqing UniversityChongqing400044P. R. China
| | - Cheng Yang
- Department of Clinical LaboratorySouthwest HospitalThird Military Medical University (Army Medical University)Chongqing400038China
| | - Dongxiao Li
- Key Laboratory of Optoelectronic Technology and SystemsMinistry of EducationInternational R&D Center of Micro‐Nano Systems and New Materials TechnologyChongqing UniversityChongqing400044P. R. China
| | - Xianming He
- Key Laboratory of Optoelectronic Technology and SystemsMinistry of EducationInternational R&D Center of Micro‐Nano Systems and New Materials TechnologyChongqing UniversityChongqing400044P. R. China
| | - He Huang
- Key Laboratory of Optoelectronic Technology and SystemsMinistry of EducationInternational R&D Center of Micro‐Nano Systems and New Materials TechnologyChongqing UniversityChongqing400044P. R. China
| | - Hong Zhou
- Key Laboratory of Optoelectronic Technology and SystemsMinistry of EducationInternational R&D Center of Micro‐Nano Systems and New Materials TechnologyChongqing UniversityChongqing400044P. R. China
- Department of Electrical and Computer EngineeringCenter for Intelligent Sensors and MEMS (CISM)NUS Graduate School for Integrative Sciences and EngineeringNational University of SingaporeSingapore117576Singapore
| | - Ming Chen
- Department of Clinical LaboratorySouthwest HospitalThird Military Medical University (Army Medical University)Chongqing400038China
| | - Chengkuo Lee
- Department of Electrical and Computer EngineeringCenter for Intelligent Sensors and MEMS (CISM)NUS Graduate School for Integrative Sciences and EngineeringNational University of SingaporeSingapore117576Singapore
| | - Xiaojing Mu
- Key Laboratory of Optoelectronic Technology and SystemsMinistry of EducationInternational R&D Center of Micro‐Nano Systems and New Materials TechnologyChongqing UniversityChongqing400044P. R. China
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23
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Hybridization chain reaction and its applications in biosensing. Talanta 2021; 234:122637. [PMID: 34364446 DOI: 10.1016/j.talanta.2021.122637] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022]
Abstract
To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.
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24
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Bodulev OL, Zhao S, Sakharov IY. Improving the Sensitivity of the miRNA Assay Coupled with the Mismatched Catalytic Hairpin Assembly Reaction by Optimization of Hairpin Annealing Conditions. Anal Chem 2021; 93:6824-6830. [PMID: 33899474 DOI: 10.1021/acs.analchem.1c00820] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mismatched catalytic hairpin assembly (mCHA), a programmable oligonucleotide circuit, is one of the promising isothermal amplification methods used in nucleic acid detection. Its limitations are related to a high background noise observed due to the target-independent hybridization of the reacting hairpins (HPs). In this work, it was shown that the introduction of salts such as NaCl and MgCl2 to HP1/HP2 annealing solutions sharply reduces the background in mCHA and simultaneously increases the signal-to-background (S/B) ratio. A comparison of the salts demonstrated the higher activity of MgCl2 as compared to NaCl. A similar effect of reducing the background was observed with a decrease in the concentration of H1/H2 probes in annealing solutions. Using the favorable annealing conditions allowed the development of an ultrasensitive chemiluminescence assay coupled with mCHA for miRNA quantitation. Except mCHA, the use of a streptavidin-polyHRP conjugate and an enhanced chemiluminescence reaction additionally increased the assay sensitivity. Notably, the optimization of the HP annealing diminished the detection limit of the assay by 2 orders of magnitude and increased the sensitivity and precision of miRNA-141 determination. The discovered fact of reducing the background by the variation of HP annealing conditions may be valuable not only for the mCHA performance but also likely for other HP-based biochemical methods.
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Affiliation(s)
- Oleg L Bodulev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, bldg. 1, Moscow 119991, Russia
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, bldg. 1, Moscow 119991, Russia
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25
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Stanciu LA, Wei Q, Barui AK, Mohammad N. Recent Advances in Aptamer-Based Biosensors for Global Health Applications. Annu Rev Biomed Eng 2021; 23:433-459. [PMID: 33872519 DOI: 10.1146/annurev-bioeng-082020-035644] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Since aptamers were first reported in the early 2000s, research on their use for the detection of health-relevant analytical targets has exploded. This review article provides a brief overview of the most recent developments in the field of aptamer-based biosensors for global health applications. The review provides a description of general aptasensing principles and follows up with examples of recent reports of diagnostics-related applications. These applications include detection of proteins and small molecules, circulating cancer cells, whole-cell pathogens, extracellular vesicles, and tissue diagnostics. The review also discusses the main challenges that this growing technology faces in the quest of bringing these new devices from the laboratory to the market.
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Affiliation(s)
- Lia A Stanciu
- School of Materials Engineering, Purdue University, West Lafayette, Indiana 47907-2045, USA; .,Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Amit K Barui
- School of Materials Engineering, Purdue University, West Lafayette, Indiana 47907-2045, USA; .,Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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26
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Ahn SY, Liu J, Vellampatti S, Wu Y, Um SH. DNA Transformations for Diagnosis and Therapy. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2008279. [PMID: 33613148 PMCID: PMC7883235 DOI: 10.1002/adfm.202008279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Indexed: 05/03/2023]
Abstract
Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.
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Affiliation(s)
- So Yeon Ahn
- School of Chemical EngineeringSungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
| | - Jin Liu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Srivithya Vellampatti
- Institute of Convergent Chemical Engineering and TechnologySungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Present address:
Progeneer, Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaSchool of Chemistry and Chemical Engineering Huazhong University of Science and Technology1037 Luoyu LoadWuhan430074China
| | - Soong Ho Um
- School of Chemical EngineeringSKKU Advanced Institute of Nanotechnology (SAINT)Biomedical Institute for Convergence at SKKU (BICS) and Institute of Quantum Biophysics (IQB)Sungkyunkwan University2066, Seobu‐ro, Jangan‐guSuwonGyeonggi‐do16419Korea
- Progeneer Inc.#1002, 12, Digital‐ro 31‐gil, Guro‐guSeoul08380Korea
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Wu L, Wang Y, Xu X, Liu Y, Lin B, Zhang M, Zhang J, Wan S, Yang C, Tan W. Aptamer-Based Detection of Circulating Targets for Precision Medicine. Chem Rev 2021; 121:12035-12105. [PMID: 33667075 DOI: 10.1021/acs.chemrev.0c01140] [Citation(s) in RCA: 240] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.
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Affiliation(s)
- Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yidi Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bingqian Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jialu Zhang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuang Wan
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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28
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Lin M, Zhang J, Wan H, Yan C, Xia F. Rationally Designed Multivalent Aptamers Targeting Cell Surface for Biomedical Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9369-9389. [PMID: 33146988 DOI: 10.1021/acsami.0c15644] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Specific interactions between ligands and receptors on cell surface play an important role in the cell biological process. Nucleic acid aptamers as commonly used ligands enable specific recognition and tight binding to membrane protein receptors for modulation of cell fate. Therefore, molecular probes with aptamers can be applied for cancer diagnosis and targeted therapy by targeting overexpression membrane proteins of cancer cells. However, because of their fast degradation and rapid glomerulus clearance in vivo, the applications of aptamers in physiological conditions remain challenged. Inspired by natural multivalent interactions, many approaches have been developed to construct multivalent aptamers to improve the performance of aptamers in complex matrices with higher binding affinity, more stability, and longer circulation time. In this review, we first introduce the aptamer generation from purified protein-based SELEX and whole cell-based SELEX for targeting the cell surface. We then highlight the approaches to fabricate multivalent aptamers and discuss their properties. By integrating different materials (including inorganic nanomaterials, diacyllipid, polymeric nanoparticles, and DNA nanostructures) as scaffolds with an interface modification technique, we have summarized four kinds of multivalent aptamers. After that, representative applications in biosensing and targeted therapy are illustrated to show the elevated performance of multivalent aptamers. In addition, we analyze the challenges and opportunities for the clinical practices of multivalent aptamers.
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Affiliation(s)
- Meihua Lin
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jian Zhang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hao Wan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Chengyang Yan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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29
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Kachwala MJ, Smith CW, Nandu N, Yigit MV. Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction. Anal Chem 2021; 93:1934-1938. [PMID: 33404234 DOI: 10.1021/acs.analchem.0c04949] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization chain reaction (HCR) is a DNA-based target-induced cascade reaction. Due to its unique enzyme-free amplification feature, HCR is often employed for sensing applications. Much like DNA nanostructures that have been designed to respond to a specific stimulus, HCR employs nucleic acids that reconfigure and assemble in the presence of a specific trigger. Despite its standalone capabilities, HCR is highly modular; therefore, it can be advanced and repurposed when coupled with latest discoveries. To this effect, we have developed a gel electrophoresis-based detection approach which combines the signal amplification feature of HCR with the programmability and sensitivity of the CRISPR-Cas12a system. By incorporating CRISPR-Cas12a, we have achieved greater sensitivity and reversed the signal output from TURN OFF to TURN ON. CRISPR-Cas12a also enabled us to rapidly reprogram the assay for the detection of both ssDNA and dsDNA target sequences by replacing a single reaction component in the detection kit. Detection of conserved, both ssDNA and dsDNA, regions of tobacco curly shoot virus (TCSV) and hepatitis B virus (HepBV) genomes is demonstrated with this methodology. This low-cost gel electrophoresis assay can detect as little as 1.5 fmol of the target without any additional target amplification steps and is about 100-fold more sensitive than HCR-alone approach.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States.,The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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30
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Su J, Liu W, Chen S, Deng W, Dou Y, Zhao Z, Li J, Li Z, Yin H, Ding X, Song S. A Carbon-Based DNA Framework Nano-Bio Interface for Biosensing with High Sensitivity and a High Signal-to-Noise Ratio. ACS Sens 2020; 5:3979-3987. [PMID: 33225707 DOI: 10.1021/acssensors.0c01745] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biosensing interface based on screen-printed carbon electrodes (SPCE) has been widely used for electrochemical biosensors in the field of medical diagnostics, food safety, and environmental monitoring. Nevertheless, SPCE always has a rough surface, which is easy to result in the disorder of nucleic acid capture probes, the nonspecific adsorption of signaling probes, the steric hindrance of target binding, and decrease in the signal-to-noise ratio and sensitivity of biosensors. So far, it still remains extremely challenging to develop high-efficiency carbon-based biosensing interfaces, especially for DNA probe-based assembly and functionalization. In this paper, we first used a specific DNA framework, DNA tetrahedron to solve the defects of the carbon interface, improving the biosensing ability of SPCE. With covalent coupling, the DNA tetrahedron could be immobilized on the carbon surface. Biosensing probe sequences extending from the DNA tetrahedron can be changed for different target molecules. We demonstrated that the improved SPCE could be applied for the detection of a variety of bioactive molecules. Typically, we designed gap hybridization, aptamer "sandwich" and aptamer competition reduction strategy for the detection of miRNA-141, thrombin, and ATP, respectively. High signal-to-noise ratio, sensitivity, and specificity were obtained for all of these kinds. Especially, the DNA tetrahedron-modified SPCE can work well with serum samples. The carbon-based DNA framework nano-bio interface would expand the use of SPCE and make electrochemical biosensors more available and valuable in clinical diagnosis.
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Affiliation(s)
- Jing Su
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wenhan Liu
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixing Chen
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
| | - Wangping Deng
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
| | - Yanzhi Dou
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihan Zhao
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
| | - Jianyong Li
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenhua Li
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Yin
- Department of Spine, TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi 214071, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shiping Song
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Institute of Applied Physics, Chinse Academy of Sciences, Shanghai 201800, China
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31
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Yan H, Zhang Z, Weng T, Zhu L, Zhang P, Wang D, Liu Q. Recognition of Bimolecular Logic Operation Pattern Based on a Solid-State Nanopore. SENSORS (BASEL, SWITZERLAND) 2020; 21:s21010033. [PMID: 33374742 PMCID: PMC7793508 DOI: 10.3390/s21010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 05/17/2023]
Abstract
Nanopores have a unique advantage for detecting biomolecules in a label-free fashion, such as DNA that can be synthesized into specific structures to perform computations. This method has been considered for the detection of diseased molecules. Here, we propose a novel marker molecule detection method based on DNA logic gate by deciphering a variable DNA tetrahedron structure using a nanopore. We designed two types of probes containing a tetrahedron and a single-strand DNA tail which paired with different parts of the target molecule. In the presence of the target, the two probes formed a double tetrahedron structure. As translocation of the single and the double tetrahedron structures under bias voltage produced different blockage signals, the events could be assigned into four different operations, i.e., (0, 0), (0, 1), (1, 0), (1, 1), according to the predefined structure by logic gate. The pattern signal produced by the AND operation is obviously different from the signal of the other three operations. This pattern recognition method has been differentiated from simple detection methods based on DNA self-assembly and nanopore technologies.
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Affiliation(s)
- Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Zhen Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Ting Weng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Pang Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
- Correspondence:
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32
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Rajwar A, Kharbanda S, Chandrasekaran AR, Gupta S, Bhatia D. Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems. ACS APPLIED BIO MATERIALS 2020; 3:7265-7277. [PMID: 35019470 DOI: 10.1021/acsabm.0c00916] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA nanotechnology is a unique field that provides simple yet robust design techniques for self-assembling nanoarchitectures with extremely high potential for biomedical applications. Though the field began to exploit DNA to build various nanoscale structures, it has now taken a different path, diverging from the creation of complex structures to functional DNA nanodevices that explore various biological systems and mechanisms. Here, we present a brief overview of DNA nanotechnology, summarizing the key strategies for construction of various DNA nanodevices, with special focus on three-dimensional (3D) nanocages or polyhedras. We then discuss biological applications of 3D DNA nanocages, particularly tetrahedral DNA cages, in their ability to program and modulate cellular systems, in biosensing, and as tools for targeted therapeutics. We conclude with a final discussion on challenges and perspectives of 3D DNA nanodevices in biomedical applications.
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Affiliation(s)
- Anjali Rajwar
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sumit Kharbanda
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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33
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Zeng Z, Zhou R, Sun R, Zhang X, Cheng Z, Chen C, Zhu Q. Nonlinear hybridization chain reaction-based functional DNA nanostructure assembly for biosensing, bioimaging applications. Biosens Bioelectron 2020; 173:112814. [PMID: 33197767 DOI: 10.1016/j.bios.2020.112814] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022]
Abstract
Hybridization chain reaction (HCR) can be divided into two categories: linear HCR and nonlinear HCR. In traditional linear HCR, the relatively slow kinetics and less sufficient sensitivity largely limit its scope of application. In the nonlinear HCR system, under the trigger of the initiator, the judicious designed substrate sequences (hairpin or hairpin-free) will self-assembly to dendritic or branched DNA nanostructures with exponential growth kinetics. Given the advantages of its enzyme-free, high-order growth kinetic, high sensitivity, and simple operation, nonlinear HCR is regarded as a powerful signal amplifier for the detection of biomarkers by integrating with versatile sensing platforms in the past few decades. In this review, we describe the basic features of nonlinear HCR mechanism and classify the nonlinear HCR into several categories based on their self-assembly mechanisms: the branched HCR, dendritic HCR, hydrogel-based clamped HCR, and other types of HCR. Then, we summarize the recent development of nonlinear HCR in biosensing, such as nucleic acid, protein, enzyme activities, and cancer cell detection, etc., and we also review the current applications of nonlinear HCR in bioimaging (mRNA in situ imaging). We choose several representative works to further illustrate the analysis mechanisms via various detection platforms, such as fluorescence, electrochemical, colorimetric, etc. At last, we also review the challenges and further perspectives of nonlinear HCR in the use of bioanalysis.
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Affiliation(s)
- Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Rong Zhou
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Ruowei Sun
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang, Hunan, China.
| | - Xun Zhang
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang, Hunan, China.
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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34
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Chen X, Xie Y, Zhang Y, Li C, Xu W. Programmable 3D rigid clathrate hydrogels based on self-assembly of tetrahedral DNA and linker PCR products. Chem Commun (Camb) 2020; 56:13181-13184. [PMID: 33020774 DOI: 10.1039/d0cc05898j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A clathrate tetrahedral DNA gel was assembled by combining tetrahedral DNA and rigid linker PCR products to achieve visible detection of Salmonella spp. This method overcame the shortcomings of AuNPs in coloration and enriched the use of tetrahedral DNA for the visible detection of virtually any target concerned with pathogens.
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Affiliation(s)
- Xu Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.
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35
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Yin C, Zhao Q, Yue A, Du W, Liu D, Zhao J, Zhang Y, Wang M. Colorimetric Detection of Class A Soybean Saponins by G-Quadruplex-Based Hybridization Chain Reaction. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2020; 2020:8813239. [PMID: 33204574 PMCID: PMC7661121 DOI: 10.1155/2020/8813239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Soybean saponin is one of the important secondary metabolites in seeds, which has various beneficial physiological functions to human health. GmSg-1 gene is the key enzyme gene for synthesizing class A saponins. It is of great significance to realize the visual and rapid detection of class A saponins at the genetic level. The hybridization chain reaction (HCR) was employed to the visual detection of GmSg-1 gene, which was implemented by changing the length of the target fragment to 92 bp and using the hairpin probes we designed to detect the GmSg-1 a and GmSg-1 b genes. The best condition of HCR reaction is hemin (1.2 μM), Triton X-100 (0.002%), ABTS (3.8 μM), and H2O2 (1.5 mM). It was found that HCR has high specificity for GmSg-1 gene and could be applied to the visual detection of different soybean cultivars containing Aa type, Ab type, and Aa/Ab type saponins, which could provide technical reference and theoretical basis for molecular breeding of soybean and development of functional soybean products.
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Affiliation(s)
- Congcong Yin
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Qiaoling Zhao
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Aiqin Yue
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Weijun Du
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Dingbin Liu
- College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jinzhong Zhao
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Yongpo Zhang
- College of Arts and Sciences, Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Min Wang
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
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36
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Lu H, Jin D, Zhu L, Guo T, Li X, Peng XX, Mo G, Tang L, Zhang GJ, Yang F. Tumor-cell detection, labeling and phenotyping with an electron-doped bifunctional signal-amplifier. Biosens Bioelectron 2020; 170:112662. [PMID: 33032198 DOI: 10.1016/j.bios.2020.112662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
Cancer cell enumeration and phenotyping can predict the prognosis and the therapy efficacy in patients, yet it remains challenging to detect the rare tumor cells. Herein, we report an octopus-inspired, bifunctional aptamer signal amplifier-based cytosensor (OApt-cytosensor) for sensitive cell analysis. By assembling high-affinity antibodies on an electrode surface, the target cells could be specifically captured and thus been sandwiched by the cell surface marker-specific DNA aptamers. These on-cell aptamers function as electrochemical signal amplifiers by base-selective electronic doping with methylene blue. Such a sandwich configuration enables highly sensitive cell detection down to 10 cells/mL (equal to ~1-2 cells at a sampling volume of 150 μL), even in a large excess of nontarget blood cells. This approach also reveals the cell-surface markers and tracks the cellular epithelial-to-mesenchymal transition induced by signaling regulators. Furthermore, the electron-doped aptamer shows remarkable cell fluorescent labeling that guides the release of the captured cells from electrode surface via electrochemistry. These features make OApt-cytosensor a promising tool in revealing the heterogeneous cancer cells and anticancer drug screening at the single-cell level.
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Affiliation(s)
- Hao Lu
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Dan Jin
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Lifei Zhu
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Tongtong Guo
- School of Pharmacy, Guangxi Medical University, Nanning, 530021, China
| | - Xinchun Li
- School of Pharmacy, Guangxi Medical University, Nanning, 530021, China.
| | - Xin-Xin Peng
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Guoyan Mo
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Lina Tang
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Guo-Jun Zhang
- College of Pharmacy, School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Fan Yang
- School of Pharmacy, Guangxi Medical University, Nanning, 530021, China.
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37
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Cheng YH, Liu SJ, Jiang JH. Enzyme-free electrochemical biosensor based on amplification of proximity-dependent surface hybridization chain reaction for ultrasensitive mRNA detection. Talanta 2020; 222:121536. [PMID: 33167244 DOI: 10.1016/j.talanta.2020.121536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 01/03/2023]
Abstract
The ability to recognize mRNA with high efficiency in cells would greatly facilitate the elucidation of mRNA-mediated cellular cascades and their disease associations. However, most traditional electrochemical strategies targeting nucleotides are always confronted with cumbersome interface operation and washing procedures, as well as the high cost of labeling and the strict reaction conditions of tool enzymes, limiting their potential applications. To address these issues, herein we reported, for the first time, a simple label-free, isothermal, non-enzymatic, and ultrasensitive homogeneous electrochemical biosensor based on autonomous proximity-dependent surface hybridization chain reaction (HCR), for sensitive signal amplification and highly specific detection of target survivin mRNA with a detection limit of 3 fM. The target triggers hybridization chain reaction and mRNA-fueled surface hybridization of ferrocene-tagged metastable DNA hairpin probes on proximity-dependent surface hybridization, resulting in the formation of multiple long-range duplex DNA chains which are immobilized onto the gold electrodes with a substantially stable ferrocene-mediated redox current. Thus, a significant electrochemical signal increase is observed dependent on the concentration of the target RNA, with a very low detection limit. Mo-reover, this molecular biosensor also exhibits excellent specificity to distinguish even single base mismatched, with strong reliability. The developed biosensor provides a novel promising tool for ultra-sensitive and selective detection, and it has great potential to be applied in mRNA-related biochemical research and clinical cancer diagnostics in more detail.
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Affiliation(s)
- Yu-Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Si-Jia Liu
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Key Laboratory of Regenerative Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, School of Basic Medical Sciences, Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, PR China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol. Mikrochim Acta 2020; 187:505. [PMID: 32815083 DOI: 10.1007/s00604-020-04471-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.
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Tang J, Lei Y, He X, Liu J, Shi H, Wang K. Recognition-Driven Remodeling of Dual-Split Aptamer Triggering In Situ Hybridization Chain Reaction for Activatable and Autonomous Identification of Cancer Cells. Anal Chem 2020; 92:10839-10846. [PMID: 32618183 DOI: 10.1021/acs.analchem.0c02524] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proximity-dependent hybridization chain reaction (HCR) has shown great potential in sensing biomolecules on the cell surface. However, the requirement of two adjacent bioevents occurring simultaneously limits its application. To solve the problem, split aptamers with target binding ability were introduced to combine with split triggers for initiating HCR, thus producing a novel dual-split aptamer probe (DSAP). By employing cancer-related receptors as models, in situ HCR on a cancer cell surface induced by recognition-driven remodeling of the DSAP was demonstrated. The DSAP consisted of two sequences. Each contained two segments; one derived from split aptamers and the other originated in split triggers. In the presence of target cells, split aptamers reassembled on the cell surface under the "induced-fit effect", thus forcing two split triggers close to each other. The remodeled DSAP worked as an intact trigger, which opened the H1 hairpin probe and then hybridized with the H2 hairpin probe, thus initiating HCR to produce an activated fluorescence signal. As a proof of concept, human liver cancer SMMC-7721 cells and their split ZY11 aptamer were used to construct the DSAP. Results indicated that the DSAP realized sensitive analysis of target cells, permitting the actual detection of 20 cells in the buffer. Moreover, the specific identification of target cells in mixed cell samples and the quantitative analysis of target cells in serum were also achieved. The DSAP strategy is facile and universal, which not only would expand the application range of HCR but also might be developed as a multitarget detection technique for bioanalysis.
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Affiliation(s)
- Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, P. R. China.,Department of Histology and Embryology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, P. R. China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, P. R. China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, P. R. China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, P. R. China
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40
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Ye D, Li M, Zhai T, Song P, Song L, Wang H, Mao X, Wang F, Zhang X, Ge Z, Shi J, Wang L, Fan C, Li Q, Zuo X. Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction. Nat Protoc 2020; 15:2163-2185. [PMID: 32572244 DOI: 10.1038/s41596-020-0326-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/06/2020] [Indexed: 11/09/2022]
Abstract
Circulating tumor cells (CTCs) enable noninvasive liquid biopsy and identification of cancer. Various approaches exist for the capture and release of CTCs, including microfluidic methods and those involving magnetic beads or nanostructured solid interfaces. However, the concomitant cell damage and fragmentation that often occur during capture make it difficult to extensively characterize and analyze living CTCs. Here, we describe an aptamer-trigger-clamped hybridization chain reaction (atcHCR) method for the capture of CTCs by porous 3D DNA hydrogels. The 3D environment of the DNA networks minimizes cell damage, and the CTCs can subsequently be released for live-cell analysis. In this protocol, initiator DNAs with aptamer-toehold biblocks specifically bind to the epithelial cell adhesion molecule (EpCAM) on the surface of CTCs, which triggers the atcHCR and the formation of a DNA hydrogel. The DNA hydrogel cloaks the CTCs, facilitating quantification with minimal cell damage. This method can be used to quantitively identify as few as 10 MCF-7 cells in a 2-µL blood sample. Decloaking of tumor cells via gentle chemical stimulus (ATP) is used to release living tumor cells for subsequent cell culture and live-cell analysis. We also describe how to use the protocol to encapsulate and release cells of cancer cell lines, which can be used in preliminary experiments to model CTCs. The whole protocol takes ~2.5 d to complete, including downstream cell culture and analysis.
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Affiliation(s)
- Dekai Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Zhai
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Song
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Lu Song
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Hua Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Joint Research Center for Precision Medicine, Shanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
| | - Zhilei Ge
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jiye Shi
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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41
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Colorimetric nanoplatform for visual determination of cancer cells via target-catalyzed hairpin assembly actuated aggregation of gold nanoparticles. Mikrochim Acta 2020; 187:392. [PMID: 32556573 DOI: 10.1007/s00604-020-04368-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/01/2020] [Indexed: 12/16/2022]
Abstract
According to aptamer-mediated hairpin DNA cascade amplifier and gold nanoparticles aggregation, an optical platform for cancer cells determination has been proposed. High-affinity chimeric aptamers were used for cancer cell detection and also as an initiator for beginning hairpin assembly to construct three-way junction (3WJ) nanostructures. These three hairpins were modified at 3' ends with biotin. In the presence of target cell, chimeric aptamer binds to its ligand on cell surface and initiates 3WJ nanostructures formation. These 3WJ nanostructures interact with streptavidin-modified gold nanoparticles (AuNPs) via non-covalent biotin-streptavidin interactions and create a crossover lattice of nanoparticles. This event leads to AuNPs aggregation and red-shifting. The results were confirmed by gel electrophoresis and UV-visible spectrophotometry. The dynamic range of this assay is 25 to 107 cells with a detection limit of 10 cells which is respectively 9 and 4 times more significant than the sensitivity of AuNP-based approaches without amplification and enzyme-mediated signal amplification. Graphical abstract.
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Yang J, Li X, Jiang B, Yuan R, Xiang Y. In Situ-Generated Multivalent Aptamer Network for Efficient Capture and Sensitive Electrochemical Detection of Circulating Tumor Cells in Whole Blood. Anal Chem 2020; 92:7893-7899. [PMID: 32338500 DOI: 10.1021/acs.analchem.0c01195] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Monitoring circulating tumor cells (CTCs) in human blood can offer useful information for convenient metastasis diagnosis, prognosis, and treatment of cancers. However, it remains a substantial challenge to detect CTCs because of their particular scarcity in complex peripheral blood. Herein, we describe an in situ-generated multivalent aptamer network-modified electrode interface for efficiently capturing and sensitively detecting CTCs in whole blood by electrochemistry. Such an interface was fabricated via rolling circle amplification extension of the electrode-immobilized primer/circular DNA complexes for the yield of long ssDNA strands with many repeated aptamer segments, which could achieve efficient capture of rare CTCs in a multivalent cooperative manner. The antibody and horseradish peroxidase-functionalized gold nanoparticles further specifically associated with the surface-bound CTCs and generated electrocatalytically amplified current outputs for highly sensitive detection of CTCs with an attractive detection limit of five cells. Also, the multivalent aptamer network interface could successfully distinguish the target cells from other control cells and achieve CTC detection in whole blood, demonstrating its promising potential for monitoring different rare CTCs in human blood.
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Affiliation(s)
- Jianmei Yang
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P. R. China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P. R. China
| | - Ruo Yuan
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yun Xiang
- School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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43
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Guo J, Lin L, Zhao K, Song Y, Huang M, Zhu Z, Zhou L, Yang C. Auto-affitech: an automated ligand binding affinity evaluation platform using digital microfluidics with a bidirectional magnetic separation method. LAB ON A CHIP 2020; 20:1577-1585. [PMID: 32207498 DOI: 10.1039/d0lc00024h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The dissociation constant (Kd) is a crucial parameter for characterizing binding affinity in molecular recognition, including antigen-antibody, DNA-protein, and receptor-ligand interactions. However, conventional methods for Kd characterization usually involve a multi-step process and time-consuming operations for incubation, washing, and detection, thus causing problems, such as time delays, microbead loss, degradation of sensitive molecules, and personal errors. Here we demonstrate an automated ligand binding affinity evaluation platform (Auto-affitech) using digital microfluidics (DMF), with individual droplets at the microliter level, programmed to rapidly perform the incubation and separation of target-beads and binding ligands. Because the loss of the beads influences the detection results, we propose a new strategy for magnetic bead separation using DMF, termed the bidirectional separation method. By splitting one droplet into two asymmetric droplets, high bead retention efficiency (89.57% ± 0.05%) and high washing efficiency (99.59% ± 0.17%, with four washings) were obtained. We demonstrate the determination of Kd of an aptamer-protein system (EpCAM and its corresponding aptamer SYL3C) and an antigen-antibody system (H5N1 antigen and antibody), proving the capability and universality of Auto-affitech in various receptor-ligand systems. Integrating all the sample processing procedures, the Auto-affitech not only saves manual labor and minimizes personal errors, but also conserves samples and shortens analysis time. Overall, this platform successfully demonstrates to be an automated approach for dissociation constant evaluation and exhibits great potential for highly efficient screening of ligands.
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Affiliation(s)
- Jingjing Guo
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Li Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Kaifeng Zhao
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mengjiao Huang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Leiji Zhou
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Chaoyong Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China. and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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44
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Xie N, Wang H, Quan K, Feng F, Huang J, Wang K. Self-assembled DNA-Based geometric polyhedrons: Construction and applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Immobilization Techniques for Aptamers on Gold Electrodes for the Electrochemical Detection of Proteins: A Review. BIOSENSORS-BASEL 2020; 10:bios10050045. [PMID: 32354207 PMCID: PMC7277302 DOI: 10.3390/bios10050045] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The development of reliable biosensing platforms plays a key role in the detection of proteins in clinically and environmentally derived samples for diagnostics, as well as for process monitoring in biotechnological productions. For this purpose, the biosensor has to be stable and reproducible, and highly sensitive to detect potentially extremely low concentrations and prevent the nonspecific binding of interfering compounds. In this review, we present an overview of recently published (2017–2019) immobilization techniques for aptamers on gold electrodes for the electrochemical detection of proteins. These include the direct immobilization of thiolated aptamers and the utilization of short linkers, streptavidin/biotin interaction, as well as DNA nanostructures and reduced graphene oxide as immobilization platforms. Applied strategies for signal amplification and the prevention of biofouling are additionally discussed, as they play a crucial role in the design of biosensors. While a wide variety of amplification strategies are already available, future investigations should aim to establish suitable antifouling strategies that are compatible with electrochemical measurements. The focus of our review lies on the detailed discussion of the underlying principles and the presentation of utilized chemical protocols in order to provide the reader with promising ideas and profound knowledge of the subject, as well as an update on recent discoveries and achievements.
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46
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DNA framework-engineered electrochemical biosensors. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1130-1141. [PMID: 32253588 DOI: 10.1007/s11427-019-1621-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023]
Abstract
Self-assembled DNA nanostructures have shown remarkable potential in the engineering of biosensing interfaces, which can improve the performance of various biosensors. In particular, by exploiting the structural rigidity and programmability of the framework nucleic acids with high precision, molecular recognition on the electrochemical biosensing interface has been significantly enhanced, leading to the development of highly sensitive and specific biosensors for nucleic acids, small molecules, proteins, and cells. In this review, we summarize recent advances in DNA framework-engineered biosensing interfaces and the application of corresponding electrochemical biosensors.
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Bakhtiari H, Palizban AA, Khanahmad H, Mofid MR. Aptamer-based approaches for in vitro molecular detection of cancer. Res Pharm Sci 2020; 15:107-122. [PMID: 32582351 PMCID: PMC7306249 DOI: 10.4103/1735-5362.283811] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
Cancer is typically associated with abnormal production of various tumor-specific molecules known as tumor markers. Probing these markers by utilizing efficient approaches could be beneficial for cancer diagnosis. The current widely-used biorecognition probes, antibodies, suffer from some undeniable shortcomings. Fortunately, novel oligonucleotide-based molecular probes named aptamers are being emerged as alternative detection tools with distinctive advantages compared to antibodies. All of the existing strategies in cancer diagnostics, including those of in vitro detection, can potentially implement aptamers as the detecting moiety. Several studies have been performed in the field of in vitro cancer detection over the last decade. In order to direct future studies, it is necessary to comprehensively summarize and review the current status of the field. Most previous studies involve only a few cancer diagnostic strategies. Here, we thoroughly review recent significant advances on the applications of aptamer in various in vitro detection strategies. Furthermore, we will discuss the status of diagnostic aptamers in clinical trials.
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Affiliation(s)
- Hadi Bakhtiari
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Abbas Ali Palizban
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Mohammad Reza Mofid
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
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An amplification strategy for detecting HER2 with a quasi-targeted proteomics approach coupled with aptamer-triggered hybridization chain reaction. Talanta 2020; 215:120918. [PMID: 32312461 DOI: 10.1016/j.talanta.2020.120918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2)-positive is a particularly aggressive type of the breast cancer. Because of the evidence has revealed that accurate HER2 status detection is crucial for prognosis and treatment strategy selection, great effort has been taken to develop assays for sensitive and accurate quantification of HER2. However, nonspecific amplification effect of most current assays limits the quantification accuracy of low abundance HER2. In the present work, we developed an LC-MS/MS-based quasi-targeted proteomics strategy coupled with hybridization chain reaction (HCR) for amplification of the HER2 protein signal. In the described strategy, the aptamer triggered the HCR system to undergo a cascade of hybridization events, with the two locked hairpins conjugated to the substrate peptide to form aptamer-HCR peptide probes. The membrane protein HER2 was recognized by probe and the signal was to be converted and then amplified into the mass response of the reporter peptide, which could be quantified using LC-MS/MS. The signal intensity was approximately five fold greater than that without signal amplification. Finally, the developed assay was applied for the quantitative analysis of HER2 in breast cell lines and monitor the dynamic change of HER2 in drug induced HER2 negative cells. The result demonstrated that combination of HCR signal amplification and mass spectrometry provides a novel approach for simple, accurate, and quantitative monitoring of low abundance protein.
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Luo L, Li W, Xiang D, Ma Y, Zhou Y, Xu Y, Chen N, Wang Q, Huang J, Liu J, Yang X, Wang K. Sensitive and specific detection of tumour cells based on a multivalent DNA nanocreeper and a multiplexed fluorescence supersandwich. Chem Commun (Camb) 2020; 56:3693-3696. [PMID: 32123883 DOI: 10.1039/c9cc08618h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A self-assembled DNA nanostructure based on a DNA nanocreeper and multiplexed fluorescence supersandwich was designed for the sensitive and specific detection of tumour cells. This nanostructure could improve the binding affinity of current aptamers and trigger signal amplification, which provide potential for the discrimination of low abundant target cells in liquid biopsy.
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Affiliation(s)
- Lei Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
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50
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Dong J, Chen JF, Smalley M, Zhao M, Ke Z, Zhu Y, Tseng HR. Nanostructured Substrates for Detection and Characterization of Circulating Rare Cells: From Materials Research to Clinical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1903663. [PMID: 31566837 PMCID: PMC6946854 DOI: 10.1002/adma.201903663] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/02/2019] [Indexed: 05/03/2023]
Abstract
Circulating rare cells in the blood are of great significance for both materials research and clinical applications. For example, circulating tumor cells (CTCs) have been demonstrated as useful biomarkers for "liquid biopsy" of the tumor. Circulating fetal nucleated cells (CFNCs) have shown potential in noninvasive prenatal diagnostics. However, it is technically challenging to detect and isolate circulating rare cells due to their extremely low abundance compared to hematologic cells. Nanostructured substrates offer a unique solution to address these challenges by providing local topographic interactions to strengthen cell adhesion and large surface areas for grafting capture agents, resulting in improved cell capture efficiency, purity, sensitivity, and reproducibility. In addition, rare-cell retrieval strategies, including stimulus-responsiveness and additive reagent-triggered release on different nanostructured substrates, allow for on-demand retrieval of the captured CTCs/CFNCs with high cell viability and molecular integrity. Several nanostructured substrate-enabled CTC/CFNC assays are observed maturing from enumeration and subclassification to molecular analyses. These can one day become powerful tools in disease diagnosis, prognostic prediction, and dynamic monitoring of therapeutic response-paving the way for personalized medical care.
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Affiliation(s)
- Jiantong Dong
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jie-Fu Chen
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Matthew Smalley
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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