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Li L, Gopinath SC, Lakshmipriya T, Subramaniam S, Anbu P. Zeolite-iron oxide integrated interdigitated electrode sensor for diagnosing cervical cancer. Heliyon 2024; 10:e31851. [PMID: 38845893 PMCID: PMC11154609 DOI: 10.1016/j.heliyon.2024.e31851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Cervical cancer is caused by changes in the cervix that lead to precancerous cells and eventually progress to cancer. Human papillomavirus (HPV) infections are the primary cause of cervical cancer. Early detection of HPV is crucial in preventing cervical cancer, and regular screening for HPV infection can identify cell changes before they develop into cancer. While Pap smear tests are reliable for cervical cancer screening, they are critical, expensive, and labor-intensive. Therefore, researchers are focusing on identifying blood-based biomarkers using biosensors for cervical cancer screening. HPV strains 16, 45, and 18 are common culprits in cervical cancer. This study aimed to develop an HPV-16 DNA biosensor on a zeolite-iron oxide (zeolite-IO) modified interdigitated electrode (IDE) sensor. The DNA probe was immobilized on the IDE through amine-modified zeolite-IO, enhancing the hybridization of the target and DNA probe. The detection limit of the DNA-DNA duplex was found to be 7.5 pM with an R2 value of 0.9868. Additionally, control experiments with single and triple mismatched sequences showed no increase in current responses, and the identification of target DNA in a serum-spiked sample indicated specific and selective target identification.
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Affiliation(s)
- Ling Li
- Obstetrics and Gynecology, Xi'an Forth Hospital, Xi'an, 710004, China
| | - Subash C.B. Gopinath
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), 02600, Arau, Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000, Kangar, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600, Arau, Perlis, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900, Penang, Malaysia
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602 105, Tamil Nadu, India
| | - Thangavel Lakshmipriya
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602 105, Tamil Nadu, India
| | - Sreeramanan Subramaniam
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), 02600, Arau, Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000, Kangar, Perlis, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900, Penang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, Georgetown, 11800, Penang, Malaysia
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Periasamy Anbu
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602 105, Tamil Nadu, India
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2
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Tan K, Chen L, Cao D, Xiao W, Lv Q, Zou L. Two-layer cascaded catalytic hairpin assemblies based on locked nucleic acids for one-step and highly sensitive ctDNA detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3515-3521. [PMID: 38774994 DOI: 10.1039/d4ay00611a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Enzyme-free signal amplification of catalytic hairpin assembly (CHA) has enabled sensitive detection of circulating tumor DNA (ctDNA) in early clinical diagnosis. Conventional CHA strategies are restrained by the limited amplification efficiency of the single-stage system, and signal leakage from "breathing" influence and nuclease degradation. Here, we introduced two-layer cascaded locked nucleic acid (LNA)-assisted CHA circuits with the intelligent incorporation of LNA in the hairpins and reporter for the highly sensitive one-step detection of scarce ctDNA. The target-triggered upstream CHA reaction continuously generates hybrid products to catalyze the downstream CHA reaction for transducing the primary sensing event, and the released target and the produced hybrid product trigger the next catalytic reaction round at the same time and finally cascade to amplify the target ctDNA fluorescence output signal. Meanwhile, the stronger binding affinity of the LNA-DNA duplex endows the two-layer LNA-assisted CHA system with thermodynamic stability and nuclease resistance, and thus our designed system exhibits an excellent detection performance for target ctDNA in the range from 2 pM to 5 nM with a low detection limit of 0.6 pM. Significantly, the two-layer LNA-assisted CHA circuits have been successfully implemented for the feasible analysis of clinical samples. This two-layer cascaded LNA-assisted CHA strategy provides a promising high sensitivity tool for one-step detection of scarce ctDNA from complex clinical samples and would facilitate the reconfiguration of DNA circuit-based DNA nanotechnology for the precise analysis of other biomarkers in clinical research fields.
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Affiliation(s)
- Kaiyue Tan
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
| | - Longsheng Chen
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
| | - Donglin Cao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-Care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou, 510500, China
| | - Wei Xiao
- Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Point-of-Care Testing (POCT), Guangdong Second Provincial General Hospital, Guangzhou, 510500, China
| | - Qian Lv
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
| | - Lili Zou
- National Engineering Research Center for Healthcare Devices, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China.
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou 510316, China
- Guangdong Provincial Key Laboratory of Medical Electronic Instruments and Polymer Material Products, Guangzhou 510316, China
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3
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Liu Q, Yang M, Zhang H, Ma W, Fu X, Li H, Gao S. A colorimetric tandem combination of CRISPR/Cas12a with dual functional hybridization chain reaction for ultra-sensitive detection of Mycobacterium bovis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3220-3230. [PMID: 38717230 DOI: 10.1039/d3ay02200e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Tuberculosis caused by Mycobacterium bovis poses a global infectious threat to humans and animals. Therefore, there is an urgent need to develop a sensitive, precise, and easy-to-readout strategy. Here, a novel tandem combination of a CRISPR/Cas12a system with dual HCR (denoted as CRISPR/Cas12a-D-HCR) was constructed for detecting Mycobacterium bovis. Based on the efficient trans-cleavage activity of the active CRISPR/Cas12a system, tandem-dsDNA with PAM sites was established using two flexible hairpins, providing multiple binding sites with CRISPR/Cas12a for further amplification. Furthermore, the activation of Cas12a initiated the second hybridization chain reaction (HCR), which integrated complete G-quadruplex sequences to assemble the hemin/G-quadruplex DNAzyme. With the addition of H2O2 and ABTS, a colorimetric signal readout strategy was achieved. Consequently, CRISPR/Cas12a-D-HCR achieved a satisfactory detection linear range from 20 aM to 50 fM, and the limit of detection was as low as 2.75 aM with single mismatched recognition capability, demonstrating good discrimination of different bacterial species. Notably, the practical application performance was verified via the standard addition method, with the recovery ranging from 96.0% to 105.2% and the relative standard deviations (RSD) ranging from 0.95% to 6.45%. The proposed CRISPR/Cas12a-D-HCR sensing system served as a promising application for accurate detection in food safety and agricultural fields.
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Affiliation(s)
- Qiong Liu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Mei Yang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - He Zhang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Wenjie Ma
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Xin Fu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Huiqing Li
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Sainan Gao
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
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4
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Qian D, Zhang J, Sun G, Zhang Y, Xu Q, Li J, Li H. Programmable Entropy-Driven Circuit-Cascaded Self-Feedback DNAzyme Network for Ultra-Sensitive Fluorescence and Photoelectrochemical Dual-Mode Biosensing. Anal Chem 2024; 96:7274-7280. [PMID: 38655584 DOI: 10.1021/acs.analchem.4c01168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Inspired by natural DNA networks, programmable artificial DNA networks have become an attractive tool for developing high-performance biosensors. However, there is still a lot of room for expansion in terms of sensitivity, atom economy, and result self-validation for current microRNA sensors. In this protocol, miRNA-122 as a target model, an ultrasensitive fluorescence (FL) and photoelectrochemical (PEC) dual-mode biosensing platform is developed using a programmable entropy-driven circuit (EDC) cascaded self-feedback DNAzyme network. The well-designed EDC realizes full utilization of the DNA strands and improves the atomic economy of the signal amplification system. The unique and rational design of the double-CdSe quantum-dot-released EDC substrate and the cascaded self-feedback DNAzyme amplification network significantly avoids high background signals and enhances sensitivity and specificity. Also, the enzyme-free, programmable EDC cascaded DNAzyme network effectively avoids the risk of signal leakage and enhances the accuracy of the sensor. Moreover, the introduction of superparamagnetic Fe3O4@SiO2-cDNA accelerates the rapid extraction of E2-CdSe QDs and E3-CdSe QDs, which greatly improves the timeliness of sensor signal reading. In addition to the strengths of linear range (6 orders of magnitude) and stability, the biosensor design with dual signal reading makes the test results self-confirming.
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Affiliation(s)
- Defu Qian
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Jingling Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Guoshuai Sun
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Yuye Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Qin Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, P. R. China
| | - Jing Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Hongbo Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
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5
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Li Y, Tang X, Deng R, Feng L, Xie S, Chen M, Zheng J, Chang K. Dumbbell Dual-Hairpin Triggered DNA Nanonet Assembly for Cascade-Amplified Sensing of Exosomal MicroRNA. ACS OMEGA 2024; 9:19723-19731. [PMID: 38708273 PMCID: PMC11064005 DOI: 10.1021/acsomega.4c02652] [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: 03/18/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Exosomal microRNAs (miRNAs) are valuable biomarkers closely associated with cancer progression. Therefore, sensitive and specific exosomal miRNA biosensing has been employed for cancer diagnosis, prognosis, and prediction. In this study, a miRNA-based DNA nanonet assembly strategy is proposed, enabling the biosensing of exosomal miRNAs through dumbbell dual-hairpin under isothermal enzyme-free conditions. This strategy dexterously designs a specific dumbbell dual-hairpin that can selectively recognize exosomal miRNA, inducing conformational changes to cascade-generated X-shaped DNA structures, facilitating the extension of the X-shaped DNA in three-dimensional space, ultimately forming a DNA nanonet assembly. On the basis of the target miRNA, our design enriches the fluorescence signal through the cascade assembly of DNA nanonet and realizes the secondary signal amplification. Using exosomal miR-141 as the target, the resultant fluorescence sensing demonstrates an impressive detection limit of 57.6 pM and could identify miRNA sequences with single-base variants with high specificity. Through the analysis of plasma and urine samples, this method effectively distinguishes between benign prostatic hyperplasia, prostate cancer, and metastatic prostate cancer. Serving as a novel noninvasive and accurate screening and diagnostic tool for prostate cancer, this dumbbell dual-hairpin triggered DNA nanonet assembly strategy is promising for clinical applications.
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Affiliation(s)
- Yongxing Li
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
- Department
of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), 183 Xinqiao, Shapingba
District, Chongqing 400037, P. R. China
- School
of Medicine, Chongqing University, Chongqing 400030, P. R. China
| | - Xiaoqi Tang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ruijia Deng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Liu Feng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Shuang Xie
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ming Chen
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ji Zheng
- Department
of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), 183 Xinqiao, Shapingba
District, Chongqing 400037, P. R. China
- School
of Medicine, Chongqing University, Chongqing 400030, P. R. China
| | - Kai Chang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
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6
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Li Y, Li C, Zhang C, Zhao L, Huang Y. Triplex DNA-based aggregation-induced emission probe: A new platform for hybridization chain reaction-based fluorescence sensing assay. Anal Chim Acta 2024; 1299:342406. [PMID: 38499412 DOI: 10.1016/j.aca.2024.342406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
The hybridization chain reaction (HCR), as one of the nucleic acid amplification technologies, is combined with fluorescence signal output with excellent sensitivity, simplicity, and stability. However, current HCR-based fluorescence sensing methods still have some defects such as the blocking effect of the HCR combination with fluorophores and the aggregation-caused quenching (ACQ) phenomenon of traditional fluorophores. Herein, a triplex DNA-based aggregation-induced emission probe (AIE-P) was designed as the fluorescent signal transduction, which is able to provide a new platform for HCR-based sensing assay. The AIE-P was synthesized by attaching the AIE fluorophores to terminus of the oligonucleotide through amido bond, and captured the products of HCR to form triplex DNA. In this case, the AIE fluorophores were located in close proximity to generate fluorescence. This assay provided turn-on fluorescence efficiency with a high signal-to-noise ratio and excellent amplification capability to solve the shortcoming of HCR-based fluorescence sensing methods. It enabled sensitive detection of Vibrio parahaemolyticus in the range of 102-106 CFU mL-1, and with a low limit of detection down to 39 CFU mL-1. In addition, this assay expressed good specificity and practicability. The triplex DNA-based AIE probe forms a universal molecular tool for developing HCR-based fluorescence sensing methods.
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Affiliation(s)
- Yubin Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China; Research Center for Coastal Environmental Protection and Ecological Resilience, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Ciling Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chuangqiang Zhang
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Liting Zhao
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yaoyun Huang
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
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7
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Zeng D, Jiao J, Mo T. Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection. Front Microbiol 2024; 15:1355234. [PMID: 38380103 PMCID: PMC10877009 DOI: 10.3389/fmicb.2024.1355234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.
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Affiliation(s)
| | | | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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8
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Peng X, He R, Xu J, Cao C, Wen W, Zhang X, Wang S. Hybridization chain reaction-enhanced electrochemically mediated ATRP coupling high-efficient magnetic separation for electrochemical aptasensing of cardiac troponin I. Anal Chim Acta 2024; 1286:342034. [PMID: 38049236 DOI: 10.1016/j.aca.2023.342034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023]
Abstract
The sensitive and accurate detection of cardiac troponin I (cTnI) as a gold biomarker for cardiovascular diseases at an early stage is crucial but has long been a challenge. In this study, we presented such an electrochemical (EC) aptasensor by combining hybridization chain reaction (HCR)-enhanced electrochemically mediated atom transfer radical polymerization (eATRP) amplification with high-efficient separation of magnetic beads (MBs). Aptamer-modified MBs empowered effective recognition and separation of cTnI from complex samples with high specificity. The specific binding of cTnI and aptamer could release triggered DNA (T-DNA) into solution to drive an HCR process, which produced plentiful active sites for eATRP initiators labeling followed by initiating eATRP process. With the development of eATRP, a great many of electroactive polymer probes were continually in situ formed to generate amplified current output for signal enhancement. Compared to no amplification, HCR-enhanced eATRP promoted the signals by ∼10-fold, greatly improving detection sensitivity for low-abundant cTnI analysis. Integrating MBs as capture carriers with HCR-enhanced eATRP as amplification strategy, this EC aptasensor achieved a low detection limit of 10.9 fg/mL for cTnI detection. Furthermore, the reliable detectability and anti-interference were confirmed in serum samples, indicating its promising application toward early diagnosis of cardiovascular diseases.
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Affiliation(s)
- Xiaolun Peng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Optoelectronic Materials and Technology, Jianghan University, 430056, Wuhan, China.
| | - Rongxiang He
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Optoelectronic Materials and Technology, Jianghan University, 430056, Wuhan, China
| | - Junhui Xu
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Optoelectronic Materials and Technology, Jianghan University, 430056, Wuhan, China
| | - Chunhua Cao
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, College of Optoelectronic Materials and Technology, Jianghan University, 430056, Wuhan, China
| | - Wei Wen
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University, 430062, Wuhan, China
| | - Xiuhua Zhang
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University, 430062, Wuhan, China
| | - Shengfu Wang
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, College of Chemistry and Chemical Engineering, Hubei University, 430062, Wuhan, China.
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9
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Zhou Y, Tang L, Lyu J, Shiyi L, Liu Q, Pang R, Li W, Guo X, Zhong X, He H. A dual signal amplification system with specific signal identification for rapid and sensitive detection of miRNA. Talanta 2024; 266:125097. [PMID: 37611369 DOI: 10.1016/j.talanta.2023.125097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/06/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
False positive which is mostly caused by the nonspecific amplification has severely hindered the development of nucleic acid detection and it is hard to avoid. Therefore, specific signals recognition and output in nucleic acid amplification are crucial to reliability of clinical diagnosis. Herein, we proposed a one-step and rapid miRNA detection strategy with specific signal identification, dual amplification and output. And this strategy was named as high-temperature hybridization chain reaction coupled with strand displacement amplification (HSA). In HSA, we well designed a target signal recognition, replication, and output probe (RRO probe). If the target miRNA exists, RRO probe can initiate a strand displacement amplification and output a target-related special single-stranded DNA (trigger). And the trigger can be identified by a high-temperature hybridization chain reaction and initiate a secondary signal amplification. As a result, the quantitative determination of HSA for miRNA-21 was in the range of 100 fM to 100 pM in 30 min, and with a detection limit of 82 fM. Moreover, with high sensitivity and rapidity, HSA has been successfully used to detect miRNA-21 in real samples.
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Affiliation(s)
- Yan Zhou
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China
| | - Jiazhen Lyu
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lixi Shiyi
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qinhao Liu
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Ruonan Pang
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Wenxin Li
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xiaolan Guo
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xiaowu Zhong
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Hongfei He
- School of Pharmacy, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Department of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China.
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10
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Bian Y, Li M, Wu Z, Weng J, Zeng R, Sun L. A natural biomaterial promotes hybridization chain reaction for ultra-sensitive detection of miRNA-155. Talanta 2024; 266:125117. [PMID: 37659230 DOI: 10.1016/j.talanta.2023.125117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023]
Abstract
MicroRNA (miRNA) is an important biomarker for early diagnosis of cancers. However, sensitive and convenient methods for miRNA detection remain a challenge. Here, we use a natural biopolymer sporopollenin purified from Ganoderma lucidum spores as a substrate for isothermal amplification (hybridization chain reaction, HCR). Sporopollenin capsules (SP) promotes HCR and forms longer and more abundant double-stranded DNA (dsDNA) than graphene oxide (GO) and carbon nanotubes (CNTs). The nanoporous structure of sporopollenin capsules containing abundant water provides a hydrous environment and enhances the hybridization efficiency of DNA significantly. We construct an ultrasensitive fluorescent biosensor to detect miR-155. The efficient HCR amplification on SP leads to an ultralow detection limit of 1 aM for miR-155 and a wide linear range of 1 aM-10 fM (R2 = 0.99). Furthermore, our fluorescence biosensor can discriminate miRNA mutants with high selectivity. This biosensor is also highly sensitive in human serum (detection limit 10 aM). It adsorbs less serum protein than GO and CNTs, thus minimizing the interference caused by the non-specific adsorption. Our study would promote medical application of SP-based biosensor in the future.
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Affiliation(s)
- Yongjun Bian
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, 422 Siming Nan Road, Xiamen, 361005, China
| | - Mengwei Li
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, 422 Siming Nan Road, Xiamen, 361005, China
| | - Zhaojie Wu
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, 422 Siming Nan Road, Xiamen, 361005, China
| | - Jian Weng
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, 422 Siming Nan Road, Xiamen, 361005, China.
| | - Ru Zeng
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, 55 Zhenhai Road, Xiamen, 361003, China
| | - Liping Sun
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, 422 Siming Nan Road, Xiamen, 361005, China.
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11
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Yang R, Liu X, Hu J, Xu H, Song J, Zhou H, Li M, Huang Y, Zhang L, Fan Q. Robust nontarget DNA-triggered catalytic hairpin assembly amplification strategy for the improved sensing of microRNA in complex biological matrices. Analyst 2023; 148:5856-5863. [PMID: 37885382 DOI: 10.1039/d3an01411h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
A simple but robust fluorescence strategy based on a nontarget DNA-triggered catalytic hairpin assembly (CHA) was constructed to probe microRNA-21 (miR-21). A short ssDNA rather than degradable target miRNA was employed as an initiator. Two molecular beacons needed to assist the CHA process were simplified to avoid unfavorable nonspecific interactions. In the presence of the target, the initiator was released from a partially duplex and triggered the cyclic CHA reaction, resulting in a significantly amplified optical readout. A wide linear range from 0.1 pM to 1000 pM for the sensing of miR-21 in buffer was achieved with a low detection limit of 0.76 pM. Fortunately, this strategy demonstrated an obviously improved performance for miR-21 detection in diluted serum. The fluorescence signals were enhanced remarkably and the sensitivity was further improved to 0.12 pM in 10% serum. The stability for miR-21 quantification and the capability for the analysis of single nucleotide polymorphisms (SNPs) were also improved greatly. More importantly, the biosensor could be applied to image miR-21 in different living tumor cells with high resolution, illustrating its promising potential for the assay of miRNAs in various complex situations for early-stage disease diagnosis and biological studies in cells.
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Affiliation(s)
- Ruining Yang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Xingfen Liu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Junbo Hu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Hui Xu
- Huzhou Key Laboratory of Green Energy Materials and Battery Cascade Utilization, School of Intelligent Manufacturing, Huzhou College, Huzhou 313000, China
| | - Jixiang Song
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Huiyu Zhou
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Meixing Li
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yanqin Huang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lei Zhang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Quli Fan
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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12
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Wang Q, Chen B, Zheng D, Xia J, Wu L, Xu J. Intramolecular Accelerated Assembly of Molecular Beacons: A DNA Nanoarchitecture-based Spatial Confinement Strategy toward Terminal Deoxynucleotidyl Transferase Biosensing. Anal Chem 2023; 95:13708-13715. [PMID: 37625083 DOI: 10.1021/acs.analchem.3c03103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Physiological function analysis of terminal deoxynucleotidyl transferase (TdT) in clinical medicine and hematopathology highlights its significance to be extensively utilized as a diagnostic biomarker for leukemia diagnosis. Herein, taking advantage of the spatial-confinement effect on a three-dimensional (3D) DNA nanoarchitecture, we reported a target-triggered intramolecular accelerated molecular beacon (MB) assembly for rapid and real-time analysis of TdT activity. In this strategy, the 3D DNA nanoarchitecture is first engineered via a cross-linking network hybridization chain reaction (HCR). A number of MBs, which were designed with a polythymine (poly-T) loop, were then conjugated on the scaffold DNA nanoarchitecture, allowing the obtained MB-DNA nanoarchitecture to contain lots of free 3'-hydroxyl (OH) termini inside or outside the super DNA nanostructure. Moreover, the distance between different MBs is closed, and the local concentration of MB is significantly improved owing to the confinement of MBs on this DNA nanoarchitecture. Once encountered with target TdT, the free -OH groups can be recognized by TdT immediately to catalyze the template-independent incorporation of adenine nucleotides, which results in the generation of multiple poly-A chains that rapidly react with many MBs via an intramolecular accelerated assembly process. The time-dependent substantial enhancement of the fluorescence from MBs can thus be applied for robustly analyzing TdT. Our observations suggest that the DNA nanostructure-based spatial confinement effect enables a high molecular collision frequency to accelerate the reaction kinetics, and the super DNA nanoarchitecture exhibits a better nuclease resistance to maintain signal stability. With these advantages, TdT can be rapidly detected with high sensitivity, specificity, and biostability.
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Affiliation(s)
- Qi Wang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui Hefei, 230601, P. R. China
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Baoqiang Chen
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Dan Zheng
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Juan Xia
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Lijun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui Hefei, 230601, P. R. China
| | - Jianguo Xu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing 314001, P. R. China
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, Hefei 230009, P. R. China
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13
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Li X, Cheng J, Zeng K, Wei S, Xiao J, Lu Y, Zhu F, Wang Z, Wang K, Wu X, Zhang Z. Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1. ACS APPLIED MATERIALS & INTERFACES 2023; 15:41237-41246. [PMID: 37625096 DOI: 10.1021/acsami.3c05506] [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: 08/27/2023]
Abstract
Traditional hybridization chain reaction (HCR) as a popular isothermal amplification technique shows some inevitable disadvantages in bioanalysis due to its relatively slow kinetics, which could be markedly promoted when the HCR initiator occurs under tension. Herein, a poly DNA tetrahedrons (pTDNs)-mediated HCR was successfully constructed to make its initiator in a stretched state by long-range electrostatic forces owing to the superimposed electrostatic interactions derived from the synthesized pTDNs, and it was hypothesized that it could remarkably enhance HCR performance, which was testified by theoretical simulations and experimental studies. Consequently, pTDNs-mediated HCR was applied to develop a novel immunoassay for rapid and sensitive detection of aflatoxin B1 as a proof-of-concept, and its signal amplification was attributed to the increased G4 DNAzyme that loaded on the second antibody. Our work paves a promising way using simple DNA frameworks alone to heighten HCR kinetics for reaction speed improvement and signal amplification in bioanalysis.
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Affiliation(s)
- Xuesong Li
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jie Cheng
- Institute of Quality Standards and Testing Technologies for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun Zeng
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Shulin Wei
- Institute of Quality Standards and Testing Technologies for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiaxuan Xiao
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yanyan Lu
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fang Zhu
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhanhui Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Kun Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiangyang Wu
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhen Zhang
- School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
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14
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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15
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2023:1-21. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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16
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Chen J, Zhang J, Xie Q, Chu Z, Zhang F, Wang Q. Ultrasensitive detection of exosomes by microchip electrophoresis combining with triple amplification strategies. Talanta 2023; 265:124930. [PMID: 37451122 DOI: 10.1016/j.talanta.2023.124930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/06/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
The analysis of exosomes is significant as they can be used for various pathophysiological processes, especially cancer related intercellular communication. Therefore, a convenient, reliable, and sensitive detection method is urgently needed. Strand displacement amplification (SDA) and catalytic hairpin assembly (CHA) are two kinds of effective isothermal nucleic acid amplification methods. In this article, an efficient quantitative MCE method for detecting human breast cancer cell (MCF-7) exosomes assisted by triple amplification strategies combining cholesterol probe (Chol-probe) with SDA-CHA was first developed. CD63 aptamer was immobilized on the avidin magnetic beads to specifically capture exosomes and then Chol-probe with high affinity was spontaneously inserted into the exosome membrane, which was the first step of amplification strategy to improve detection sensitivity. After magnetic separation, Chol-probe could complement ssDNA and trigger SDA, producing a large number of DNA sequences (Ta) to trigger CHA, achieving SDA-CHA amplification. Under optimal conditions, the detection limit (LOD) for MCF-7 exosomes was as low as 26 particle/μL (S/N = 3). This method provides an effective approach for sensitive and accurate quantification of tumor exosomes, and can be expected to detect exosomes in clinical samples.
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Affiliation(s)
- Jingyi Chen
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Jingzi Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Qihui Xie
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Zhaohui Chu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China.
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China.
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17
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Anbiaee G, Khoshbin Z, Zahraee H, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Exonuclease-based aptasensors: Promising for food safety and diagnostic aims. Talanta 2023; 259:124500. [PMID: 37001398 DOI: 10.1016/j.talanta.2023.124500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023]
Abstract
As of today's requirement, developing cost-effective smart sensing tools with ultrahigh sensitivity for food safety insurance is of special importance. For this purpose, aptamer-based biosensors (aptasensors) powered by the superiorities of the recycling signal amplification strategies have been expanded especially. Target recycling supported by enzymes is an appealing approach for implementing signal amplification. As the supreme biocatalyst enzymes, exonucleases can inaugurate signal improvement by involving a single target in a process would result in appreciable repeating cycles of the cleavage of the phosphodiester bonds between the building blocks of the nucleic acid strands, and also, their terminals. Although there are diverse substances for catalyzing amplification strategies, including nanoparticles, carbon-based nanocomposites, and quantum dots (QDs), exonucleases are of superiority over them by simplifying the amplification process with no need for the complicated pre-treatment processes. The outstanding selectivity and great sensitivity of the aptasensors tuned by amplification potency of exonucleases nominate them as the promising sensing tools for label-free, ease-of-use, cost-effective, and real-time diagnosis of diverse targets. Here, we summarize the achievements and perspectives in the scientific branch of aptasensor design for the qualitative monitoring of diverse targets by cooperation of exonucleases with the conspicuous potential for the signal amplification. Finally, some results are expressed to provide a comprehensive viewpoint for developing novel nuclease-based aptasensors in the future.
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Affiliation(s)
- Ghasem Anbiaee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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18
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Du H, Li X, Xu S, Cheng G, Xue Q, Xu H. N/S-Co-doped carbon dot-based FRET ratiometric fluorescence aptasensing platform modulated with entropy-driven DNA amplifier for ochratoxin A detection. Anal Bioanal Chem 2023:10.1007/s00216-023-04778-5. [PMID: 37306781 DOI: 10.1007/s00216-023-04778-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 06/13/2023]
Abstract
This study proposes a nitrogen and sulfur co-doped carbon dot (N/S-CD)-based FRET ratiometric fluorescence aptasensing strategy modulated with entropy-driven DNA amplifier for sensitive and accurate detection of ochratoxin A (OTA). In the strategy, a duplex DNA probe containing OTA aptamer and complementary DNA (cDNA) is designed as a recognition and transformation element. Upon sensing of target OTA, the cDNA was liberated, and triggered a three-chain DNA composite-based entropy-driven DNA circuit amplification, making CuO probes anchor on a magnetic bead (MB). The CuO-encoded MB complex probe is finally turned into abundant Cu2+, which oxidizes o-phenylenediamine (oPD) to generate 2,3-diaminophenazine (DAP) with yellow fluorescence and further triggers FRET between the blue fluorescent N/S-CDs and DAP. The changes in ratiometric fluorescence are related to the OTA concentration. Originating from the synergistic amplifications from the entropy-driven DNA circuits and Cu2+ amplification, the strategy dramatically enhanced detection performance. A limit of detection as low as 0.006 pg/mL of OTA was achieved. Significantly, the aptasensor can visually evaluate the OTA via on-site visual screening. Moreover, the high-confidence quantification of the OTA in real samples with results consistent with that of the LC-MS method indicated that the proposed strategy has practical application prospects for sensitive and accurate quantification in food safety.
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Affiliation(s)
- Huiyan Du
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Shuling Xu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Guiguang Cheng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Hongxia Xu
- Department of Clinical Laboratory, The Third People's Hospital of Liaocheng, Liaocheng, 252059, Shandong, China.
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19
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Song Z, Zhang QY, Li JJ, Su JL, Liu YH, Yang GJ, Wang HS. Visual and Electrochemical Detection of let-7a: A Tumor Suppressor and Biomarker. J Med Chem 2023. [PMID: 37248170 DOI: 10.1021/acs.jmedchem.3c00499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Let-7a, a type of low-expressed microRNAs in cancer cells, has been investigated as a promising biomarker and therapeutic target for tumor suppression. Developing simple and sensitive detection methods for let-7a is important for cancer diagnosis and treatment. In this work, the hybridization chain reaction (HCR) was initiated by let-7a via two hairpin primers (H1 and H2). After the HCR, the remaining hairpin H1 was further detected by lateral flow assay (LFA) and electrochemical impedance spectroscopy. For LFA, biotin-modified H1(bio-H1) and free H2 were used for HCR. With the decrease of let-7a concentration, the color of T line gradually increased. As for electrochemical methods, the H1'-AuNP-modified electrode was used for detection of bio-H1 based on the difference of impedance (ΔRct) detected without and with different concentrations of let-7a participating in the HCR. This method could detect let-7a in the range of 10.0 fM and 1.0 nM with detection limits of 4.2 fM.
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Affiliation(s)
- Zhen Song
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Qiang-Yan Zhang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jia-Jing Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jing-Lian Su
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yuan-Hua Liu
- Department of Chemotherapy, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing 210009, P. R. China
| | - Gong-Jun Yang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Huai-Song Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
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20
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Shi G, Yan C, Chen J. Fluorescent aptasensor for the ultrasensitive detection of antibiotic residue in food samples based on dumbbell DNA-mediated signal amplification. Biosens Bioelectron 2023; 228:115188. [PMID: 36871423 DOI: 10.1016/j.bios.2023.115188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/05/2023]
Abstract
Sensitive and reliable detection of antibiotics is of great significance for environmental and food safety due to its high risk in trace concentrations. Herein, we developed a fluorescence sensing system for chloramphenicol (CAP) detection based on dumbbell DNA-mediated signal amplification. Two hairpin dimers (2H1 and 2H2) were employed as the building blocks to construct the sensing scaffolds. The CAP-aptamer binding in another hairpin H0 can liberate the trigger DNA, which then activates the cyclic assembly reaction between 2H1 and 2H2. The separation of FAM and BHQ in the formed product of cascaded DNA ladder yields a high fluorescence signal for CAP monitoring. Compared with the monomer hairpin assembly between H1 and H2, the dimer hairpin assembly between 2H1 and 2H2 exhibits enhanced signal amplification efficiency and reduced reaction time. The developed CAP sensor showed a wide linear range from 10 fM to 10 nM with a detection limit of 2 fM. Importantly, this sensing platform has been successfully applied to the determination of CAP in fish, milk, and water samples with satisfactory recovery and accuracy. With the advantages of high sensitivity, mix-and-read pattern, and robustness, our proposed CAP sensor can be used as a simple and routine tool for the detection of trace amounts of antibiotic residues.
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Affiliation(s)
- Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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21
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Ning W, Zhang C, Tian Z, Wu M, Luo Z, Hu S, Pan H, Li Y. Ω-shaped fiber optic LSPR biosensor based on mismatched hybridization chain reaction and gold nanoparticles for detection of circulating cell-free DNA. Biosens Bioelectron 2023; 228:115175. [PMID: 36871422 DOI: 10.1016/j.bios.2023.115175] [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: 10/19/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Circulating cell-free DNA (cfDNA) is a promising biomarker of liquid biopsy, but it still faces some difficulties in achieving sensitive and convenient detection. Herein, an Ω-shaped fiber optic localized surface plasmon resonance (FO-LSPR) biosensor based on hybridization chain reaction (HCR) coupled with gold nanoparticles (AuNPs) was developed, and applied in simple and sensitive detection of cfDNA. Specifically, one-base mismatch was designed in HCR hairpins (H1 and H2) to obtain high reaction efficiency, and AuNPs was introduced onto H1 through poly-adenine to construct HCR coupled with AuNPs strategy. Meanwhile, target cfDNA was designed into two domains: one could trigger HCR to generate dsDNA concatemer carrying numerous AuNPs, and the other could hybridize with capture DNA on the surface of Ω-shaped fiber optic (FO) probes. Thus, the presence of target cfDNA would initiate HCR, and bring the formed dsDNA concatemer and AuNPs to approach the probe surface, resulting in dramatically amplified LSPR signal. Besides, HCR required simple isothermal and enzyme-free condition, and Ω-shaped FO probe with high refractive index sensitivity just needed to be immersed into HCR solution directly for signal monitoring. Benefiting from the synergetic amplification of mismatched HCR and AuNPs, the proposed biosensor exhibited high sensitivity with a limit of detection of 14.0 pM, and therefore could provide a potential strategy for biomedical analysis and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuyan Zhang
- Medical Equipment Innovation Research Center, Precision Medicine Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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22
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Xia N, Cheng J, Tian L, Zhang S, Wang Y, Li G. Hybridization Chain Reaction-Based Electrochemical Biosensors by Integrating the Advantages of Homogeneous Reaction and Heterogeneous Detection. BIOSENSORS 2023; 13:bios13050543. [PMID: 37232904 DOI: 10.3390/bios13050543] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
The conventional hybridization chain reaction (HCR)-based electrochemical biosensors usually require the immobilization of probes on the electrode surface. This will limit the applications of biosensors due to the shortcomings of complex immobilization processes and low HCR efficiency. In this work, we proposed astrategy for the design of HCR-based electrochemical biosensors by integrating the advantages of homogeneous reaction and heterogeneous detection. Specifically, the targets triggered the autonomous cross-opening and hybridization oftwobiotin-labeled hairpin probes to form long-nicked dsDNA polymers. The HCR products with many biotin tags were then captured by a streptavidin-covered electrode, thus allowing for the attachment of streptavidin-conjugated signal reporters through streptavidin-biotin interactions. By employing DNA and microRNA-21 as the model targets and glucose oxidase as the signal reporter, the analytical performances of the HCR-based electrochemical biosensors were investigated. The detection limits of this method were found to be 0.6 fM and 1 fM for DNA and microRNA-21, respectively. The proposed strategy exhibited good reliability for target analysis in serum and cellular lysates. The strategy can be used to develop various HCR-based biosensors for a wide range of applications because sequence-specific oligonucleotides exhibit high binding affinity to a series of targets. In light of the high stability and commercial availability of streptavidin-modified materials, the strategy can be used for the design of different biosensors by changing the signal reporter and/or the sequence of hairpin probes.
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Affiliation(s)
- Ning Xia
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Jiayou Cheng
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Linxu Tian
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Shuo Zhang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Yunqiu Wang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Gang Li
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
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23
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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24
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Wang S, Li H, Dong K, Shu W, Zhang J, Zhang J, Zhao R, Wei S, Feng D, Xiao X, Zhang W. A universal and specific RNA biosensor via DNA circuit-mediated PAM-independent CRISPR/Cas12a and PolyA-rolling circle amplification. Biosens Bioelectron 2023; 226:115139. [PMID: 36774734 DOI: 10.1016/j.bios.2023.115139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Point of care testing (POCT) has important clinical significance for the diagnosis and prognosis evaluation of diseases. At present, the biosensor based on CRISPR/Cas12a has become a powerful diagnostic tool due to its high sensitivity. However, CRISPR/Cas12a requires PAM sequence to recognize target double strand and only can recognize specific sequence, so it is not universal. The current RNA detection techniques either lack consideration for specificity and universality, are expensive and difficult, or both. Therefore, it is crucial to create a CRISPR/Cas12a-based RNA detection system that is easy to use, cheap, specific, and universal in order to further its use in molecular diagnostics. Here, we established a DNA circuit-mediated PAM-independent CRISPR/Cas12a coupled PolyA-rolling circle amplification for RNA detection biosensor, namely DCPRBiosensor. The DCPRBiosensor not only functions as a simple, inexpensive, and highly sensitive RNA detection sensor, but it also boasts innovative specificity and universality features. More importantly, DCPRBiosensor removes the PAM restriction of CRISPR/Cas12a. The DCPRBiosensor's detection limit reached 100 aM and it had a linear relationship between 100 aM and 10 pM. We detected four piRNAs to verify the universality and stability of DCPRBiosensor. Then, we verified that DCPRBiosensor has good discrimination ability for single-base mismatch. Finally, we successfully detected piRNA in DLD-1 and HCT-116 cells and urine mixed samples within 4.5 h. In conclusion, we believe that DCPRBiosensor will have a substantial impact on both the development of CRISPR/as12a's applications and the investigation of the clinical value of piRNA.
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Affiliation(s)
- Sidan Wang
- Queen Mary School, Nanchang University, Nanchang, 330006, China
| | - Haojia Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jiarui Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Dilu Feng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
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25
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Fu X, Chen Z, Ma W, Zhang H, Mo W, Li J, Yang M. Entropy-driven dynamic self-assembled DNA dendrimers for colorimetric detection of African swine fever virus. Anal Bioanal Chem 2023; 415:1675-1685. [PMID: 36715708 DOI: 10.1007/s00216-023-04562-5] [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: 10/26/2022] [Revised: 01/04/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023]
Abstract
Herein, we subtly engineered an amplified colorimetric biosensor for the cyclic detection of African swine fever virus DNA (ASFV-DNA), which associated the branched catalytic hairpin assembly (bCHA) amplification with G-quadruplex DNAzyme activity through triplex DNA formation. Firstly, a Y-shaped hairpin trimer was constructed for the dynamic self-assembly of DNA dendrimers. Then, in the presence of ASFV-DNA, the signal strand CP was opened, exposing the toehold regions, which would trigger the CHA cascade reaction between hairpin trimers. In the CHA cascade reaction, H1, H2, and H3 opened and bound in sequence, eventually forming the structure of DNA dendrimers. Subsequently, the obtained bCHA product was specifically recognized by the GGG repeat sequences of L1 and L2, then amplified by the synergistic effect of triplex DNA and the formation of asymmetric split G-quadruplex. Benefiting from the amplification properties of bCHA and the high peroxidase-like catalytic activity of asymmetrically split G-quadruplex DNAzymes, it could achieve effective colorimetric signal output in the presence of ASFV-DNA by means of triplex DNA formation. Under the optimal experimental conditions, this biosensor exhibited excellent sensitivity with a detection limit of 1.8 pM. Further, it was applied to the content detection of simulated samples of African swine fever, and the recoveries were 98.9 ~ 103.2%. This method has the advantages of simple operation, good selectivity, and high sensitivity, which is expected to be used for highly sensitive detection of actual samples of African swine fever virus.
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Affiliation(s)
- Xin Fu
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Zhoujie Chen
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Wenjie Ma
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - He Zhang
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Wenhao Mo
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Jinyan Li
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Mei Yang
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
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26
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Ma L, Liao D, Zhao Z, Kou J, Guo H, Xiong X, Man S. Sensitive Small Molecule Aptasensing based on Hybridization Chain Reaction and CRISPR/Cas12a Using a Portable 3D-Printed Visualizer. ACS Sens 2023; 8:1076-1084. [PMID: 36651835 DOI: 10.1021/acssensors.2c02097] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Next-generation biosensing tools based on CRISPR/Cas have revolutionized the molecular detection. A number of CRISPR/Cas-based biosensors have been reported for the detection of nucleic acid targets. The establishment of efficient methods for non-nucleic acid target detection would further broaden the scope of this technique, but up to now, the concerning research is limited. In the current study, we reported a versatile biosensing platform for non-nucleic acid small-molecule detection called SMART-Cas12a (small-molecule aptamer regulated test using CRISPR/Cas12a). Simply, hybridization chain reaction cascade signal amplification was first trigged by functional nucleic acid (aptamer) through target binding. Then, the CRISPR/Cas system was integrated to recognize the amplified products followed by activation of the trans-cleavage. As such, the target can be ingeniously converted to nucleic acid signals and then fluorescent signals that can be readily visualized and analyzed by a customized 3D-printed visualizer with the help of a home-made App-enabled smartphone. Adenosine triphosphate was selected as a model target, and under the optimized conditions, we achieved fine analytical performance with a linear range from 0.1 to 750 μM and a detection limit of 1.0 nM. The satisfactory selectivity and recoveries that we have obtained further demonstrated this method to be suitable for a complex sample environment. The sample-to-answer time was less than 100 min. Our work not only expanded the reach of the CRISPR-Cas system in biosensing but also provided a prototype method that can be generalized for detecting a wider range of analytes with desirable adaptability, sensitivity, specificity, and on-site capability.
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Affiliation(s)
- Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Dan Liao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Haoyu Guo
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xin Xiong
- College of Artificial Intelligence, Tianjin University of Science and Technology, Tianjin 3000457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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27
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Zhang Z, Jia X, Xu X. An electrochemical aptasensor for detection of streptomycin based on signal amplification assisted by functionalized gold nanoparticles and hybridization chain reaction. Mikrochim Acta 2023; 190:152. [PMID: 36959354 DOI: 10.1007/s00604-023-05737-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/08/2023] [Indexed: 03/25/2023]
Abstract
A ratiometric electrochemical aptasensor based on gold nanoparticles (AuNPs) functionalization and hybridization chain reaction (HCR) assisted signal amplification has been for the first time designed for the detection of streptomycin (STR). The double-stranded DNA (dsDNA) formed by the hybridization of ferrocene (Fc)-labeled STR aptamer (Apt) and capture probe (CP) is first immobilized on the gold electrode (GE) surface via Au-S reaction. The specific binding of the target and Apt results in numerous Fc detachment from the sensing interface. Then, the remaining single-stranded CP is combined with AuNPs modified with initiator DNA (iDNA) by auxiliary DNA (aDNA). Among them, the iDNA triggers HCR between two hairpin probes (H1/H2), thus capturing a large number of methylene blue (MB) electrochemical probe, which generates a strong electrochemical signal of MB and a weak electrochemical signal of Fc. Signals are collected by square wave voltammetry (the potential window ranging from -0.5 V to 0.6 V, vs. Ag/AgCl ), and the oxidation peak currents at -0.200 V (MB) and 0.416 V (Fc) are recorded. The use of the ratiometric method has effectively improved the accuracy and reliability of the analysis. The successful application of AuNPs and HCR greatly improves the sensitivity of the sensor, and the detection limit is as low as 0.08 pM. It can sensitively determine STR in the range 0.1 pM to 10 nM. In addition, the designed aptasensor has been successfully applied to the detection of STR in milk and honey samples.
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Affiliation(s)
- Zhoubing Zhang
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Xiaorun Jia
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Xueqin Xu
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350108, Fujian, China.
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28
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Yang FA, Wu YT, Liu YW, Liao WC. Hybridization chain reaction-assisted enzyme cascade genosensor for the detection of Listeria monocytogenes. Talanta 2023; 254:124193. [PMID: 36549135 DOI: 10.1016/j.talanta.2022.124193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Foodborne diseases caused by pathogens may threaten public health and the social economy. We demonstrated a method for identifying pathogenic Listeria monocytogenes using DNA logic operations. To achieve accurate species distinguishing, three specific sequences of Listeria monocytogenes genomic DNA were screened out and used as the feature sequences. Three complementary probes with tag modification were designed as sensing elements and exert affinity for magnetic beads, glucose oxidase (GOx), and horseradish peroxidase (HRP). To obtain a digital output (YES/NO answer) for rapid determination, a Boolean logic function was employed. Three sensing probes enabled the recognition of the target sequence (input) and the formation of a target DNA/probe hybrid. Through magnetic separation and affinity binding events, the target DNA/probes hybrid led to the construction of GOx/HRP enzyme cascade, which produced a visualized color signal (output) in the presence of substrates, glucose, and 3, 3', 5, 5'-tetramethylbenzidine (TMB). A hybridization chain reaction (HCR) was coupled with this sensing scaffold to increase the binding of the enzyme cascade and amplify the output signal. The logical functional biosensor showed high selectivity of Listeria monocytogenes over other Listeria species. This sensing platform provides a simple, sensitive, and highly specific method for detecting Listeria monocytogenes.
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Affiliation(s)
- Fu-An Yang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yi-Ting Wu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Yen-Wenn Liu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Wei-Ching Liao
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Medical Device Innovation and Translation Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
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29
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Wang B, Wang M, Peng F, Fu X, Wen M, Shi Y, Chen M, Ke G, Zhang XB. Construction and Application of DNAzyme-based Nanodevices. Chem Res Chin Univ 2023; 39:42-60. [PMID: 36687211 PMCID: PMC9841151 DOI: 10.1007/s40242-023-2334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Menghui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaoyi Fu
- Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, 310022 P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Yuyan Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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30
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Zhang Z, Zhang L, Liu Y, Hu C, Liu Q. Sensitive DNA Detection using a Branched DNA as a Sensor Coupled with Hybridization Chain Reaction. ChemistrySelect 2022. [DOI: 10.1002/slct.202201891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhikun Zhang
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Liu Zhang
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Yumin Liu
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Cuixia Hu
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Qingju Liu
- Beijing Research Center for Agriculture Standards and Testing Beijing Academy of Agriculture and Forestry Sciences Beijing 100097 China
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31
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Zhang Y, Li R, Yu S, Shang J, He Y, Wang Y, Liu X, Wang F. Sensitive Autocatalytic Hybridization Circuit for Reliable In Situ Intracellular Polynucleotide Kinase Imaging. Anal Chem 2022; 94:13951-13957. [PMID: 36170650 DOI: 10.1021/acs.analchem.2c03169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Exploring the characteristic functions of polynucleotide kinase (PNK) could substantially promote the elucidation of PNK-related mechanistic pathways. Yet, the sensitive and reliable detection of intracellular PNK still presents a challenging goal. Herein, we propose a simple autocatalytic hybridization circuit (AHC) for in situ intracellular imaging of PNK with high reliability. The AHC amplifier consists of two mutually activated hybridization chain reaction (HCR) modules for magnified signal transduction. The PNK is transduced into initiator I by phosphorylation and cleavage of mediator Hp. Initiator I activates the initial HCR-1 module, leading to the formation of long dsDNA nanowires that carry numerous initiator T. Then, T-initiated feedback HCR-2 module generates branched products that contain plentiful initiator I, thus realizing an autocatalytic HCR amplification reaction. Simultaneously, the HCR-2 module is also assembled as a versatile signal transduction unit for generating the amplified readout. Based on the mutually sustained accumulation of two initiators for the reciprocal activation of two reaction modules, continuous signal amplification and assembly of high-molecular-weight copolymers endow the AHC system with high sensitivity and robustness for the PNK assay. Moreover, the PNK-sensing AHC system achieves reliable imaging of intracellular PNK, thus showing great potential to decipher the correlation between PNK and related diseases.
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Affiliation(s)
- Yanping Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430072, P. R. China
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Strategies for Enhancing the Sensitivity of Electrochemiluminescence Biosensors. BIOSENSORS 2022; 12:bios12090750. [PMID: 36140135 PMCID: PMC9496703 DOI: 10.3390/bios12090750] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022]
Abstract
Electrochemiluminescence (ECL) has received considerable attention as a powerful analytical technique for the sensitive and accurate detection of biological analytes owing to its high sensitivity and selectivity and wide dynamic range. To satisfy the growing demand for ultrasensitive analysis techniques with high efficiency and accuracy in complex real sample matrices, considerable efforts have been dedicated to developing ECL strategies to improve the sensitivity of bioanalysis. As one of the most effective approaches, diverse signal amplification strategies have been integrated with ECL biosensors to achieve desirable analytical performance. This review summarizes the recent advances in ECL biosensing based on various signal amplification strategies, including DNA-assisted amplification strategies, efficient ECL luminophores, surface-enhanced electrochemiluminescence, and ratiometric strategies. Sensitivity-enhancing strategies and bio-related applications are discussed in detail. Moreover, the future trends and challenges of ECL biosensors are discussed.
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Zhu C, Zhang F, Li H, Chen Z, Yan M, Li L, Qu F. CRISPR/Cas Systems Accelerating the Development of Aptasensors. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Liu Y, Wang C, Zhang C, Chen R, Liu B, Zhang K. Nonenzymatic Multiamplified Electrochemical Detection of Medulloblastoma-Relevant MicroRNAs from Cerebrospinal Fluid. ACS Sens 2022; 7:2320-2327. [PMID: 35925869 DOI: 10.1021/acssensors.2c00956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The sensitive analysis of microRNAs (miRNAs) in cerebrospinal fluid (CSF) holds promise for the minimally invasive early diagnosis of brain cancers such as pediatric medulloblastoma but remains challenging due partially to a lack of facile yet sensitive sensing methods. Herein, an enzyme-free triple-signal amplification electrochemical assay for miRNA was developed by integrating the target-triggered cyclic strand-displacement reaction (TCSDR), hybridization chain reaction (HCR), and methylene blue (MB) intercalation. In this assay, the presence of target miRNA (miR-9) initiated the TCSDR and produced primers that triggered the subsequent HCR amplification to generate copious double-stranded DNAs (dsDNAs) on the electrode surface. Intercalation of a large number of MB reporters into the long nicked double helixes of dsDNAs yielded a more enhanced signal of differential pulse voltammetry. The enzyme-free multiple-amplification approach allowed for highly sensitive (detection limit: 6.5 fM) and sequence-specific (single-base mismatch resolution) detection of miR-9 from tumor cells and human CSF with minimal sample consumption (10 μL). Moreover, the clinical utilization of this method was documented by accurate discrimination of five medulloblastoma patients from the nontumoral controls. In light of its sensitivity, specificity, and convenience of use, this electrochemical method was expected to facilitate the early detection of malignant brain tumors.
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Affiliation(s)
- Yujie Liu
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chen Wang
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chenran Zhang
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ruoping Chen
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences Fudan University, Shanghai 200438, China
| | - Kun Zhang
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
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Geng X, Chen J, Chu Z, Zhang J, Zhang F, Wang Q. Highly sensitive detection of MUC1 by microchip electrophoresis combining with target recycling amplification and strand displacement amplification. J Pharm Biomed Anal 2022; 219:114967. [PMID: 35914507 DOI: 10.1016/j.jpba.2022.114967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
Mucin 1 (MUC1) is usually overexpressed in a variety of malignant tumors, and quantitative analysis of MUC1 plays an important role in the early diagnosis of cancer. In this work, a highly sensitive MUC1 assay was developed by integrating microchip electrophoresis (MCE) with target recycling amplification (TRA) and strand displacement amplification (SDA). Specifically, the presence of MUC1 can trigger the exposure of the designed hairpin probe (HP) to initiate SDA and an amplified amount of ssDNA is produced finally. The amount of these ssDNA can be detected by MCE, then the concentration of MUC1 can be obtained through the correlation between MUC1 concentration and ssDNA concentration. The experimental results show that the MCE signal had a good linear relationship with MUC1 concentration in the range of 1.0 pg/mL - 1.0 × 103 pg/mL with a low limit of detection of 0.23 pg/mL under the optimal conditions (S/N = 3). Additionally, the assay had been successfully applied to detect MUC1 in biological samples with satisfactory results, providing an alternative assay for the detection of other tumor markers owing to the high sensitivity, high selectivity, simple operation and low sample consumption.
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Affiliation(s)
- Xing Geng
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jingyi Chen
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Zhaohui Chu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jingzi Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
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Aptamer-antibody hybrid ELONA that uses hybridization chain reaction to detect a urinary biomarker EN2 for bladder and prostate cancer. Sci Rep 2022; 12:11523. [PMID: 35798816 PMCID: PMC9263169 DOI: 10.1038/s41598-022-15556-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022] Open
Abstract
We report an EN2-specific (Kd = 8.26 nM) aptamer, and a sensitive and specific enzyme-linked oligonucleotide assay (ELONA) for rapid and sensitive colorimetric detection of bladder and prostate cancer biomarker EN2 in urine. The assay relies on an aptamer-mediated hybridization chain reaction (HCR) to generate DNA nanostructures that bind to EN2 and simultaneously amplify signals. The assay can be performed within 2.5 h, and has a limit of detection of 0.34 nM in buffer and 2.69 nM in artificial urine. Moreover, this assay showed high specificity as it did not detect other urinary proteins, including biomarkers of other cancers. The proposed ELONA is inexpensive, highly reproducible, and has great chemical stability, so it may enable development of a simple, sensitive and accurate diagnostic tool to detect bladder and prostate cancers early.
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Xu L, Zhao W, Pu J, Wang S, Liu S, Li H, Yu R. A Pax-5a gene analysis approach enabled by selective digestion with lambda exonuclease. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2415-2422. [PMID: 35670541 DOI: 10.1039/d2ay00469k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Owing to the rapid increase in acute leukemia patients, the detection of Pax-5a, which is a tumor marker, is very important for the early diagnosis of patients. Therefore, by combining the selective digestion function of lambda exonuclease and the hybridization chain reaction (HCR) enzyme-free amplification system, we design a biosensor to detect the Pax-5a gene with high sensitivity. Lambda exonuclease can cleave the blunt end formed by the hairpin probe and the Pax-5a gene, which exposes the nucleic acid sequence that can initiate the HCR. When the HCR is triggered, the fluorophore and quencher on H1 and H2 move away from each other, so that the fluorescence signal of the quenched fluorophore can be recovered. Under optimal experimental conditions, a good linear relationship was established between the fluorescence intensity and the logarithm of the target concentration, and the limit of detection (LOD) of Pax-5a was calculated to be 7.6 pM. In addition, the biosensor can not only discriminate the base mismatch sequences of the Pax-5a gene, but also be suitable for target detection in complex human serum samples. Therefore, this biosensor, with the advantages of simple operation, high sensitivity, and good selectivity, has a good application prospect and guiding role in the diagnosis of acute B lymphocytic leukemia and the design of biosensors.
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Affiliation(s)
- LianLian Xu
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Weihua Zhao
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Jiamei Pu
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Suqin Wang
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Shiwen Liu
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, P. R. China
| | - Hongbo Li
- Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China.
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou 215123, P. R. China
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
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38
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Li S, Cheng Y, Qin M, Zhou G, Li P, Yang L. Intelligent and robust DNA robots capable of swarming into leakless nonlinear amplification in response to a trigger. NANOSCALE HORIZONS 2022; 7:634-643. [PMID: 35527720 DOI: 10.1039/d2nh00018k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nonlinear DNA signal amplification with an enzyme-free isothermal self-assembly process is uniquely useful in nanotechnology and nanomedicine. However, progress in this direction is hampered by the lack of effective design models of leak-resistant DNA building blocks. Here, we propose two conceptual models of intelligent and robust DNA robots to perform a leakless nonlinear signal amplification in response to a trigger. Two conceptual models are based on super-hairpin nanostructures, which are designed by innovating novel principles in methodology and codifying them into embedded programs. The dynamical and thermodynamical analyses reveal the critical elements and leak-resistant mechanisms of the designed models, and the leak-resistant behaviors of the intelligent DNA robots and morphologies of swarming into nonlinear amplification are separately verified. The applications of the designed models are also illustrated in specific signal amplification and targeted payload enrichment via integration with an aptamer, a fluorescent molecule and surface-enhanced Raman spectroscopy. This work has the potential to serve as design guidelines of intelligent and robust DNA robots and leakless nonlinear DNA amplification, and also as the design blueprint of cargo delivery robots with the performance of swarming into nonlinear amplification in response to a target automatically, facilitating their future applications in biosensing, bioimaging and biomedicine.
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Affiliation(s)
- Shaofei Li
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- School of Life Science, Anhui University, Hefei 230601, Anhui, China
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Yizhuang Cheng
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Miao Qin
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Guoliang Zhou
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Pan Li
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
| | - Liangbao Yang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui, China
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Xu R, Cheng Y, Li X, Zhang Z, Zhu M, Qi X, Chen L, Han L. Aptamer-based signal amplification strategies coupled with microchips for high-sensitivity bioanalytical applications: A review. Anal Chim Acta 2022; 1209:339893. [DOI: 10.1016/j.aca.2022.339893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023]
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40
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Lu Y, Rong X, Wu P, Shou J, Chen L, Luo F, Lin C, Wang J, Qiu B, Lin Z. Sensitive Electrochemiluminescence Biosensor Based on the Target Trigger Difference of the Electrostatic Interaction between an ECL Reporter and the Electrode Surface. Anal Chem 2022; 94:5823-5829. [PMID: 35385271 DOI: 10.1021/acs.analchem.1c05258] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The discrepancy of the electrostatic interaction of negatively charged signal molecules to long and short DNA strands of the modified electrode surface has been used for the first time to the develop an electrochemiluminescence (ECL) biosensor for human papillomavirus 16 (HPV 16) DNA detection. The short single-stranded capture probe (CP) was modified first on the surface of the gold electrode, which only has a small amount of negative charge. The electrostatic interaction between the negatively charged tris(2,2'-bipyridyl) ruthenium(II) chloride hexahydrate-doped SiO2 nanoparticles (Ru@SiO2 NPs) and CP is weak, hence Ru@SiO2 NPs easily diffuse to the surface of the electrode to generate a strong ECL signal. Hybrid chain reaction (HCR) amplification products (long strand dsDNA) were prepared in homogeneous solution in advance. When the target was present, the dsDNA can be connected on the electrode surface and cause the enhancement of the negative charge on the electrode surface. Owing to electrostatic interaction and steric hindrance, Ru@SiO2 NPs are difficult to diffuse to the electrode surface, resulting in a significantly reduced ECL signal. The decrease of ECL signal is linearly correlated with the logarithm of the HPV concentration under optimal conditions, with the detection range being 0.1 fM -5 pM with a limit of 1.41 aM. This innovative methodology expands the application of electrostatic interaction in ECL sensing, but can also easily develop biosensors for detecting other targets by changing the DNA sequence used in this strategy.
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Affiliation(s)
- Yilei Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Xiujun Rong
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Peng Wu
- Department of Obstetrics and Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang 311201, China
| | - Jian Shou
- Department of Obstetrics and Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang 311201, China
| | - Long Chen
- Department of Obstetrics and Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang 311201, China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Cuiying Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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41
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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42
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Pusta A, Tertis M, Graur F, Cristea C, Al Hajjar N. Aptamers and New Bioreceptors for the Electrochemical Detection of Biomarkers Expressed in Hepatocellular Carcinoma. Curr Med Chem 2022; 29:4363-4390. [PMID: 35196969 DOI: 10.2174/0929867329666220222113707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/11/2021] [Accepted: 12/18/2021] [Indexed: 11/22/2022]
Abstract
Hepatocellular carcinoma is a malignancy associated with high mortality and increasing incidence. Early detection of this disease could help increase survival and overall patient benefit. Non-invasive strategies for the diagnosis of this medical condition are of utmost importance. In this scope, the detection of hepatocellular carcinoma biomarkers could provide a useful diagnostic tool. Aptamers represent as short, single-stranded DNAs or RNAs that can specifically bind selected analytes, and also as pseudo-biorecognition elements that can be employed for electrode functionalization. Also, other types of DNA sequences can be used for the construction of DNA-based biosensors applied for the quantification of hepatocellular carcinoma biomarkers. Herein, we will be analyzing recent examples of aptasensors and DNA biosensors for the detection of hepatocellular carcinoma biomarkers like micro-RNAs, long non-coding RNAs, exosomes, circulating tumor cells and proteins. The literature data is discussed comparatively in a critical manner highlighting the advantages of using electrochemical biosensors in diagnosis, as well as the use of nanomaterials and biocomponents in the functionalization of electrodes for improved sensitivity and selectivity.
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Affiliation(s)
- Alexandra Pusta
- Department of Analytical Chemistry, Faculty of Pharmacy,"Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Medical Devices, Faculty of Pharmacy,"Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca,Romania
| | - Mihaela Tertis
- Department of Analytical Chemistry, Faculty of Pharmacy,"Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Florin Graur
- Department of Surgery, Iuliu Hațieganu University of Medicine and Pharmacy Romania
| | - Cecilia Cristea
- Department of Medical Devices, Faculty of Pharmacy,"Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca,Romania
| | - Nadim Al Hajjar
- Department of Surgery, Iuliu Hațieganu University of Medicine and Pharmacy Romania
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43
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Dual-mode amplified fluorescence oligosensor mediated MOF-MoS2 for ultra-sensitive simultaneous detection of 17β -estradiol and chloramphenicol through catalytic target- recycling activity of exonuclease I. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106971] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Zhang L, Su W, Liu S, Huang C, Ghalandari B, Divsalar A, Ding X. Recent Progresses in Electrochemical DNA Biosensors for MicroRNA Detection. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:18-32. [PMID: 36939771 PMCID: PMC9590547 DOI: 10.1007/s43657-021-00032-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs), as the small, non-coding, evolutionary conserved, and post-transcriptional gene regulators of the genome, have been highly associated with various diseases such as cancers, viral infections, and cardiovascular diseases. Several techniques have been established to detect miRNAs, including northern blotting, real-time polymerase chain reaction (RT-PCR), and fluorescent microarray platform. However, it remains a significant challenge to develop sensitive, accurate, rapid, and cost-effective methods to detect miRNAs due to their short size, high similarity, and low abundance. The electrochemical biosensors exhibit tremendous potential in miRNA detection because they satisfy feature integration, portability, mass production, short response time, and minimal sample consumption. This article reviewed the working principles and signal amplification strategies of electrochemical DNA biosensors summarized the recent improvements. With the development of DNA nanotechnology, nanomaterials and biotechnology, electrochemical DNA biosensors of high sensitivity and specificity for microRNA detection will shortly be commercially accessible.
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Affiliation(s)
- Lulu Zhang
- Institute of Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Wenqiong Su
- Institute of Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Shuopeng Liu
- East China Branch, China Academy of Information and Communications Technology, Shanghai, 200030 China
| | - Chengjie Huang
- Institute of Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Behafarid Ghalandari
- Institute of Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Adeleh Divsalar
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, 15719-14911 Iran
| | - Xianting Ding
- Institute of Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
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Wu M, Zhang C, Tian Z, Xie Q, Lu X, Ning W, Li Y, Duan Y. A universal array platform for ultrasensitive, high-throughput and microvolume detection of heavy metal, nucleic acid and bacteria based on photonic crystals combined with DNA nanomachine. Biosens Bioelectron 2022; 197:113731. [PMID: 34768068 DOI: 10.1016/j.bios.2021.113731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/19/2021] [Accepted: 10/23/2021] [Indexed: 01/07/2023]
Abstract
The development of a universal, sensitive, and rapid assay platform to achieve detections of heavy metal, nucleic acid and bacteria is of great significance but it also faces a thorny challenge. Herein, a novel and universal array platform was developed by combining photonic crystals (PCs) and DNA nanomachine. The developed array platform integrated the physical and biological signal amplification ability of PCs and DNA nanomachine, resulting in ultrasensitive detections of Hg2+, DNA, and Shigella sonnei with limits of detection (LODs) of 22.1 ppt, 31.6 fM, and 9 CFU/mL, respectively. More importantly, by utilizing a microplate reader as signal output device, the array achieved high-throughput scanning (96 samples/3 min) with only 2 μL loading sample, which is advantageous for the detection of infectious dangerous targets. In addition, the PCs array could be obtained easily and rapidly based on self-assembly of colloidal nanospheres, and the DNA nanomachine was operated with enzyme-free and time-saving features. Benefiting from these merits, the proposed PCs array offered a powerful universal platform for large-scale detection of various analytes in the fields of pollution monitoring, epidemic control, and public health.
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Affiliation(s)
- Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Chuyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiyue Xie
- College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Xiaoyong Lu
- College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China.
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Arshavsky‐Graham S, Heuer C, Jiang X, Segal E. Aptasensors versus immunosensors—Which will prevail? Eng Life Sci 2022; 22:319-333. [PMID: 35382545 PMCID: PMC8961048 DOI: 10.1002/elsc.202100148] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/11/2022] Open
Abstract
Since the invention of the first biosensors 70 years ago, they have turned into valuable and versatile tools for various applications, ranging from disease diagnosis to environmental monitoring. Traditionally, antibodies have been employed as the capture probes in most biosensors, owing to their innate ability to bind their target with high affinity and specificity, and are still considered as the gold standard. Yet, the resulting immunosensors often suffer from considerable limitations, which are mainly ascribed to the antibody size, conjugation chemistry, stability, and costs. Over the past decade, aptamers have emerged as promising alternative capture probes presenting some advantages over existing constraints of immunosensors, as well as new biosensing concepts. Herein, we review the employment of antibodies and aptamers as capture probes in biosensing platforms, addressing the main aspects of biosensor design and mechanism. We also aim to compare both capture probe classes from theoretical and experimental perspectives. Yet, we highlight that such comparisons are not straightforward, and these two families of capture probes should not be necessarily perceived as competing but rather as complementary. We, thus, elaborate on their combined use in hybrid biosensing schemes benefiting from the advantages of each biorecognition element.
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Affiliation(s)
- Sofia Arshavsky‐Graham
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Christopher Heuer
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Xin Jiang
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Ester Segal
- Faculty of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
- Russell Berrie Nanotechnology Institute Technion ‐ Israel Institute of Technology Haifa Israel
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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: 71] [Impact Index Per Article: 35.5] [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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48
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Fan Z, Yao B, Ding Y, Xu D, Zhao J, Zhang K. Rational engineering the DNA tetrahedrons of dual wavelength ratiometric electrochemiluminescence biosensor for high efficient detection of SARS-CoV-2 RdRp gene by using entropy-driven and bipedal DNA walker amplification strategy. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2022; 427:131686. [PMID: 34400874 PMCID: PMC8349740 DOI: 10.1016/j.cej.2021.131686] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/20/2021] [Accepted: 08/01/2021] [Indexed: 05/06/2023]
Abstract
Fast and effective detection of epidemics is the key to preventing the spread of diseases. In this work, we constructed a dual-wavelength ratiometric electrochemiluminescence (ECL) biosensor based on entropy-driven and bipedal DNA walker cycle amplification strategies for detection of the RNA-dependent RNA polymerase (RdRp) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The entropy-driven cyclic amplification reaction was started by the SARS-CoV-2 RdRp gene to generate a bandage. The bandage could combine with two other single-stranded S1 and S2 to form a bipedal DNA walker to create the following cycle reaction. After the bipedal DNA walker completed the walking process, the hairpin structures at the top of the DNA tetrahedrons (TDNAs) were removed. Subsequently, the PEI-Ru@Ti3C2@AuNPs-S7 probes were used to combine with the excised hairpin part of TDNAs on the surface of Au-g-C3N4, and the signal change was realized employing electrochemiluminescence resonance energy transfer (ECL-RET). By combining entropy-driven and DNA walker cycle amplification strategy, the ratiometric ECL biosensor exhibited a limit of detection (LOD) as low as 7.8 aM for the SARS-CoV-2 RdRp gene. As a result, detecting the SARS-CoV-2 RdRp gene in human serum still possessed high recovery so that the dual-wavelength ratiometer biosensor could be used in early clinical diagnosis.
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Affiliation(s)
- Zhenqiang Fan
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Bo Yao
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Yuedi Ding
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Dong Xu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Jianfeng Zhao
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China
| | - Kai Zhang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
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Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging.
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Affiliation(s)
- Anastasia A. Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, 141701, Russia
| | - Victor M. Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Valeria A. Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Georgiy Yu. Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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Jing L, Xie C, Li Q, Yang M, Li S, Li H, Xia F. Electrochemical Biosensors for the Analysis of Breast Cancer Biomarkers: From Design to Application. Anal Chem 2021; 94:269-296. [PMID: 34854296 DOI: 10.1021/acs.analchem.1c04475] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Le Jing
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Chongyu Xie
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Qianqian Li
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meiqing Yang
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shaoguang Li
- State Key Laboratory of Biogeology Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hui Li
- State Key Laboratory of Biogeology Environmental Geology, 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
- State Key Laboratory of Biogeology Environmental Geology, 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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