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Yang C, Shi Y, Zhang Y, He J, Zhang Z, Jia X, Yuan R, Xu W. A bivariate fluorescence biosensor based on Janus DNA nanoarchitecture-loaded dual-emissive Ag nanoclusters as bi-responsive signaling reporters. Biosens Bioelectron 2024; 263:116621. [PMID: 39098283 DOI: 10.1016/j.bios.2024.116621] [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: 06/20/2024] [Revised: 07/27/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
Constructing label-free bivariate fluorescence biosensor would be intriguing and desired for the recognizable and accurate detection of two specific DNA segments, yet the design of functional DNA structures with low overlapped interference might be challenging. Herein in this work, a double-faced Janus DNA nanoarchitecture (JDNA) with bi-responsive recognition regions on opposite sides was assembled, which consisted of two substrate strands and two template strands for loading green-/red-emissive Ag nanoclusters (gAgNC and rAgNC) as bivariate signaling reporters. Of note, the hybridized double helix in the middle rationally oriented two flank faces and stabilized the rigid conformation of JDNA, while the template sequences of bicolor clusters were blocked to minimize non-specific background leakage. Upon inputting two targets, the discernible hairpins lost their hairpin structures due to forming two dsDNA complexes. They were executed to simultaneously invade JDNA for activating two individual target-recycled strand displacement (TRSD) events, guiding signal transduction and efficient amplification. Consequently, the clustering templates were unlocked via the tailored conformation switch of JDNA, in which gAgNC and rAgNC were in situ synthesized in two diagonal positions, thereby significantly emitting bi-responsive signal without cross interference. Benefited from the logic integration of double-faced JDNA and TRSD, a label-free, sensitive and specific bivariate fluorescence approach was developed, which would open a new avenue for the potential application in biosensing and bioanalysis.
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Affiliation(s)
- Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Yanan Shi
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Zhihan Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xinyue Jia
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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2
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Wu C, Hao Z, Deng H, Jiang Y, Yuan R, Yuan Y. AgI Precipitation Induced Polarity Reversal with Formation of Z-Type Heterojunction for Photoelectrochemical Sensing. Anal Chem 2024; 96:14759-14765. [PMID: 39234645 DOI: 10.1021/acs.analchem.4c01577] [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: 09/06/2024]
Abstract
Regulating photocurrent polarity is highly attractive for fabricating photoelectrochemical (PEC) biosensors with improved sensitivity and accuracy in practical samples. Here, a new approach that adopts the in situ generated AgI precipitate and AgNCs to reversal Bi2WO6 polarity with formation of Z-type heterojunction was proposed for the first time, which coupled with a high-efficient target conversion strategy of exonuclease III (Exo III)-assisted triple recycling amplification for sensing miRNA-21. The target-related DNA nanospheres in situ generated on electrode with loading of plentiful AgI and AgNCs not only endowed the photocurrent of Bi2WO6 switching from the anodic to cathodic one due to the changes in the electron transfer pathway but also formed AgI/AgNCs/Au/Bi2WO6 Z-type heterojunction to improve the photoelectric conversion efficiency for acquiring extremely enhanced PEC signal, thereby significantly avoiding the problem of high background signal derived from traditional unidirectional increasing/decreasing response and false-positive/false-negative. Experimental data showed that the PEC biosensor had a low detection limit down to 0.085 fM, providing a new polarity-reversal mechanism and expected application in diverse fields, including biomedical research and clinical diagnosis.
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Affiliation(s)
- Chou Wu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Zhipeng Hao
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing 400042, P.R. China
| | - Hanmei Deng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ying Jiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yali Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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Zhao XY, Liu LL, Xu YQ, Xiang L, Yuan R, Chai YQ. Dual-Ligand Europium-Organic Gels as a Highly Efficient Anodic Annihilation Electrochemiluminescence Emitter for Ultrasensitive Detection of MicroRNA. Anal Chem 2024; 96:9961-9968. [PMID: 38838250 DOI: 10.1021/acs.analchem.4c01239] [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: 06/07/2024]
Abstract
In this study, a novel europium dual-ligand metal-organic gel (Eu-D-MOGs) with high-efficient anodic annihilation electrochemiluminescence (ECL) was synthesized as an ECL emitter to construct a biosensor for ultrasensitive detection of microRNA-221 (miR-221). Impressively, compared to the ECL signal of europium single-ligand metal-organic gels (Eu-S-MOGs), the ECL signal of Eu-D-MOGs was significantly improved since the two organic ligands could jointly replace the H2O and coordinate with Eu3+, which could remarkably reduce the nonradiative vibrational energy transfer caused by the coordination between H2O and Eu3+ with a high coordination demand. In addition, Eu-D-MOGs could be electrochemically oxidized to Eu-D-MOGs•+ at 1.45 V and reduced to Eu-D-MOGs•- at 0.65 V to achieve effective annihilation of ECL, which overcame the side reaction brought by the remaining emitters at negative potential. This benefited from the annihilation ECL performance of the central ion Eu3+ caused by its redox in the electrochemical process. Furthermore, the annihilation ECL signal of Eu3+ could be improved by sensitizing Eu3+ via the antenna effect. In addition, combined with the improved rolling circle amplification-assisted strand displacement amplification strategy (RCA-SDA), a sensitive biosensor was constructed for the sensitive detection of miR-221 with a low detection limit of 5.12 aM and could be successfully applied for the detection of miR-221 in the lysate of cancer cells. This strategy offered a unique approach to synthesizing metal-organic gels as ECL emitters without a coreactant for the construction of ECL biosensing platforms in biomarker detection and disease diagnosis.
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Affiliation(s)
- Xin-Yan Zhao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Lin-Lei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Yuan-Qi Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Lian Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
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4
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Zhu D, Zhao D, Hu Y, Wei T, Su T, Su S, Chao J, Wang L. Programmably engineered stochastic RNA nanowalker for ultrasensitive miRNA detection. Chem Commun (Camb) 2024; 60:6142-6145. [PMID: 38804211 DOI: 10.1039/d4cc01656d] [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: 05/29/2024]
Abstract
A programmably engineered stochastic RNA nanowalker powered by duplex-specific nuclease (DSN) is developed. By utilizing poly-adenine-based spherical nucleic acids (polyA-SNA) to accurately regulate the densities of DNA tracks, the nanowalker showcases its capability to identify miRNA-21, miRNA-486, and miRNA-155 with quick kinetics and attomolar sensitivity, positioning it as a promising option for cancer clinical surveillance.
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Affiliation(s)
- Dan Zhu
- 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, 9 Wenyuan Road, Nanjing 210023, China.
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Dongxia Zhao
- 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, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yang Hu
- 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, 9 Wenyuan Road, Nanjing 210023, China.
| | - Tianhui Wei
- 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, 9 Wenyuan Road, Nanjing 210023, China.
| | - Tong Su
- 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, 9 Wenyuan Road, Nanjing 210023, China.
| | - Shao Su
- 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, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jie Chao
- 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, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lianhui Wang
- 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, 9 Wenyuan Road, Nanjing 210023, China.
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5
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Xia L, Chen J, Hou X, Zhou R, Cheng N. Construction of a streptavidin-based dual-localized DNAzyme walker for disease biomarker detection. Chem Commun (Camb) 2024; 60:5848-5851. [PMID: 38752318 DOI: 10.1039/d4cc00912f] [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: 05/31/2024]
Abstract
A dual-localized DNAzyme walker (dlDW) was constructed by utilizing multiple split DNAzymes with probes, and their substrates are separately localized on streptavidin and AuNPs, serving as walking pedals and tracks, respectively. Based on dlDW, biosensing platform was successfully constructed and showed great potential application in clinical disease diagnosis.
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Affiliation(s)
- Lingying Xia
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiandeng Hou
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rongxing Zhou
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Nansheng Cheng
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Dai C, Mao Z, Xu Y, Jia J, Tang H, Zhao Y, Zhou Y. Bis-tridentate Iridium(III) Complex with the N-Heterocyclic Carbene Ligand as a Novel Efficient Electrochemiluminescence Emitter for the Sandwich Immunoassay of the HHV-6A Virus. Anal Chem 2024; 96:7311-7320. [PMID: 38656817 DOI: 10.1021/acs.analchem.4c01431] [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
Human herpesvirus type 6A (HHV-6A) can cause a series of immune and neurological diseases, and the establishment of a sensitive biosensor for the rapid detection of HHV-6A is of great significance for public health and safety. Herein, a bis-tridentate iridium complex (BisLT-Ir-NHC) comprising the N-heterocyclic carbene (NHC) ligand as a novel kind of efficient ECL luminophore has been unprecedently reported. Based on its excellent ECL properties, a new sensitive ECL-based sandwich immunosensor to detect the HHV-6A virus was successfully constructed by encapsulating BisLT-Ir-NHC into silica nanoparticles and embellishing ECL sensing interface with MXene@Au-CS. Notably, the immunosensor illustrated in this work not only had a wide linear range of 102 to 107 cps/μL but also showed outstanding recoveries (98.33-105.11%) in real human serum with an RSD of 0.85-3.56%. Undoubtedly, these results demonstrated the significant potential of the bis-tridentate iridium(III) complex containing an NHC ligand in developing ECL-based sensitive analytical methods for virus detection and exploring novel kinds of efficient iridium-based ECL luminophores in the future.
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Affiliation(s)
- Chenji Dai
- School of Chemistry and Life Sciences, Jiangsu Key Laboratory for Environmental Functional Materials, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Ziwang Mao
- School of Chemistry and Life Sciences, Jiangsu Key Laboratory for Environmental Functional Materials, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Yaoyao Xu
- School of Chemistry and Life Sciences, Jiangsu Key Laboratory for Environmental Functional Materials, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Junli Jia
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Huamin Tang
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yibo Zhao
- School of Chemistry and Life Sciences, Jiangsu Key Laboratory for Environmental Functional Materials, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Yuyang Zhou
- School of Chemistry and Life Sciences, Jiangsu Key Laboratory for Environmental Functional Materials, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
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Wang S, Liu Y, Liu R, Xie L, Yang H, Ge S, Yu J. Strand displacement amplification triggered 3D DNA roller assisted CRISPR/Cas12a electrochemiluminescence cascaded signal amplification for sensitive detection of Ec-16S rDNA. Anal Chim Acta 2024; 1291:342213. [PMID: 38280789 DOI: 10.1016/j.aca.2024.342213] [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: 11/14/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND Escherichia coli can cause gastrointestinal infection, urinary tract infection and other infectious diseases. Accurate detection of Escherichia coli 16S rDNA (Ec-16S rDNA) in clinical practice is of great significance for the identification and treatment of related diseases. At present, there are various types of sensors that can achieve accurate detection of Ec-16S rDNA. Electrochemiluminescence (ECL) has attracted considerable attention from researchers, which causes excellent performance in bioanalysis. Based on the previous research, it is significance to develop a novel, sensitive and efficient ECL biosensor. RESULTS In this work, an ECL biosensor for the detection of Ec-16S rDNA was constructed by integrating CRISPR/Cas12a technology with the cascade signal amplification strategy consisting of strand displacement amplification (SDA) and dual-particle three-dimensional (3D) DNA rollers. The amplification products of SDA triggered the operation of the DNA rollers, and the products generated by the DNA rollers activated CRISPR/Cas12a to cleave the signal probe, thereby realizing the change of the ECL signal. The cascade amplification strategy realized the exponential amplification of the target signal and greatly improved the sensitivity. Manganese dioxide nanoflowers (MnO2 NFs) as a co-reaction promoter effectively enhanced the ECL intensity of tin disulfide quantum dots (SnS2 QDs). A new ternary ECL system (SnS2 QDs/S2O82-/MnO2 NFs) was prepared, which made the change of ECL intensity of biosensor more significant. The proposed biosensor had a response range of 100 aM-10 nM and a detection limit of 27.29 aM (S/N = 3). SIGNIFICANCE AND NOVELTY Herein, the cascade signal amplification strategy formed by SDA and dual-particle 3D DNA rollers enabled the ECL biosensor to have high sensitivity and low detection limit. At the same time, the cascade signal amplification strategy was integrated with CRISPR/Cas12a to enable the biosensor to efficiently detect the target. It can provide a new idea for the detection of Ec-16S rDNA in disease diagnosis and clinical analysis.
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Affiliation(s)
- Shujing Wang
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, PR China
| | - Yaqi Liu
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, PR China
| | - Ruifang Liu
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, PR China
| | - Li Xie
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, PR China.
| | - Hongmei Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, PR China.
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
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Wang Y, Zou M, Chen Y, Tang F, Dai J, Jin Y, Wang C, Xue F. Ultrasensitive and selective detection of sulfamethazine in milk via a Janus-labeled Au nanoparticle-based surface-enhanced Raman scattering-immunochromatographic assay. Talanta 2024; 267:125208. [PMID: 37717540 DOI: 10.1016/j.talanta.2023.125208] [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: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Sulfamethazine (SM2) is an antibacterial drug,which has been extensively used in human and veterinary medicine, long-term consumption of which may lead to the accumulation of sulfonamides in the body. Detection of sulfonamides often uses microbiological approaches, mass spectrometry and chromatography, which are expensive and time-consuming. Surface-enhanced Raman scattering-based immunochromatographic assay (SERS-ICA) has been recently applied in the detection. Herein, a Janus-labeled Au nanoparticle with subnanosized SiO2-monoclonal antibody and SERS reporter (DTNB) modified simultaneously (mAbAuNpDTNB) has been developed in a SERS-based lateral flow immunosensor, which can be used for rapid, quantitative and ultrasensitive detection of sulfamethazine residue in milk. The mAbAuNpDTNB exhibits a specific array on a paper stripe, which not only identifies sulfamethazine but also straightforwardly exposes the Raman reporter between the AuNps via self-assembly. The detection sensitivity of SERS-ICA for sulfamethazine reached 0.1 pg/mL, which was far below the previously published value by ELISA and the maximum residue limit set by the European Union. The entire SERS-ICA detection for sulfamethazine was completed within 15 min. Furthermore, high accuracy for this assay was exhibited in the spiking experiment with a recovery percentage of 88.1%-112.7%. The results demonstrated that this SERS-ICA can potentially be applied in point-of-care testing as an ultrasensitive and quantitative to semi-quantitative analytical method.
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Affiliation(s)
- Yufeng Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Chinese Academy of Inspection and Quarantine (CAIQ), No. A3, Gaobeidian Road, Chaoyang District, Beijing, 100123, China; Sanya Institute of Nanjing Agricultural University, Sanya, 572025, China
| | - Mingqiang Zou
- Chinese Academy of Inspection and Quarantine (CAIQ), No. A3, Gaobeidian Road, Chaoyang District, Beijing, 100123, China
| | - Yan Chen
- Chinese Academy of Inspection and Quarantine (CAIQ), No. A3, Gaobeidian Road, Chaoyang District, Beijing, 100123, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Jin
- Chinese Academy of Inspection and Quarantine (CAIQ), No. A3, Gaobeidian Road, Chaoyang District, Beijing, 100123, China.
| | - Cong Wang
- Beijing Key Laboratory of Microstructure and Properties of Solids, Faculty of Materials and Manufacturing, Beijing University of Technology, Beijing, 100124, China.
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; Sanya Institute of Nanjing Agricultural University, Sanya, 572025, China.
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9
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Huang X, Li Z, Shi Y, Zhang Y, Shen T, Chen M, Huang Z, Tong Y, Liu SY, Guo J, Zou X, Dai Z. A DNAzyme dual-feedback autocatalytic exponential amplification biocircuit for microRNA imaging in living cells. Biosens Bioelectron 2023; 241:115669. [PMID: 37688849 DOI: 10.1016/j.bios.2023.115669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/21/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023]
Abstract
Autocatalytic biocircuit are powerful tools for analysing intracellular biomarkers, but these tools are constrained by limitations in amplification capacity and intracellular delivery efficiency. In this work, we developed a DNAzyme-based dual-feedback autocatalytic exponential amplification biocircuit sustained by a honeycomb MnO2 nanosponge (EDA2@hMNS) for live-cell imaging of intracellular low-abundance microRNAs (miRNA). The EDA2 biocircuit comprises a blocked DNAzyme (b-DNAzyme), a Fuel strand and a Substrate strand. In the EDA2 biocircuit, target miRNAs are recycled and feedback for rounds of DNAzymatic amplification, and the DNAzymatic reactions continuously generate target miRNA analogues for dual-feedback to achieve multiple parallel cascade DNAzymatic reactions that improve amplification capacity substantially. In addition, the hMNS ensures high loading and delivery efficiency of biocircuit probes into living cells and also provides sufficient Mn2+ DNAzyme cofactor from in situ decomposition by intracellular glutathione (GSH). The EDA2@hMNS realized a detection limit of 17 pM, which is 288-fold lower than the b-DNAzyme lacking the DNAzymatic amplification. These results demonstrate the great promise for this critical tool in analysing low-abundance biomarkers and cancer diagnostics.
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Affiliation(s)
- Xing Huang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zihao Li
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yakun Shi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Taorong Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Meng Chen
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zhan Huang
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanli Tong
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Si-Yang Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jianhe Guo
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China.
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10
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Wang H, Yang B, Tang H, Ding S, Liu G. Hairpin DNA-based electrochemical amplification strategy for miRNA sensing by using single gold nanoelectrodes. Analyst 2023; 148:5636-5641. [PMID: 37846736 DOI: 10.1039/d3an01551c] [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: 10/18/2023]
Abstract
A new sensor has been developed to detect miRNA-15 using nanoelectrodes and a hairpin DNA-based electrochemical amplification technique. By utilizing a complex DNA cylinder connected with hairpin DNA1, the sensor is able to absorb more methylene blue (MB) than simple double-stranded DNA. Another hairpin DNA2 is modified on an Au nanoelectrode surface and, when miRNA-15 is introduced, it triggers a chain reaction. This reaction unlocks two hairpins alternatively to polymerize into a complex structure that attaches more MB. The miRNA-15 is then replaced by DNA1 due to strand displacement reactions and continues to react with the next DNA2 to achieve circular amplification. The electrochemical signal from MB oxidation has a linear relationship with the miRNA-15 concentrations, making it possible to detect miRNA-15. Moreover, this method can be readily adapted for the detection of various other miRNA species. The newly devised nanosensor holds promising applications for the in vivo detection of miRNA-15 within biological systems, which is achieved by leveraging the advantageous characteristics of nanoelectrodes, including their low resistance-capacitance time constant, rapid mass transfer kinetics, and small diameter.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Binbin Yang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Haoran Tang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Sufang Ding
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
| | - Gen Liu
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education; School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui 235000, P R China.
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11
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Meng R, Zhang X, Liu J, Zhou Y, Zhang P, Chai Y, Yuan R. Dual-layer 3D DNA nanostructure: The next generation of ultrafast DNA nanomachine for microRNA sensing and intracellular imaging. Biosens Bioelectron 2023; 237:115517. [PMID: 37459686 DOI: 10.1016/j.bios.2023.115517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 07/04/2023] [Indexed: 08/13/2023]
Abstract
The working efficiency of traditional 3D DNA nanomachines is extremely restricted due to the complex DNA components modified on nanoparticles in the same spatial height. Herein, an ultrafast dual-layer 3D DNA nanomachine (UDDNM) based on catalytic hairpin assembly (CHA) was developed by assembling two different lengths of hairpin DNA on the surface of gold nanoparticles, the long hairpin 1 (H1), to capture the trigger, and the short hairpin 2 (H2), as the signal probe, to recycle the trigger. Compared to the traditional single-layer 3D DNA nanomachine, the dual-layer 3D DNA nanostructure greatly enhances the effective collision between trigger and targeted DNA probe, H1, since the H1 located in outer layer would react with the trigger, inhibiting the invalid collision between the trigger and residual DNA component, H2, and remarkably decreasing the steric hindrance associated with the nucleic acids layer around the nanoparticles. Especially, when the distance of two layers was fixed at 3 nm, the corresponding UDDNM could accomplish the overall reaction only in 3 min with a dramatically high initial rate of up to 5.93 × 10-7 M s-1, which was at least 5-fold beyond that of the typical single-layer 3D DNA nanomachines. As a proof of concept, the described UDDNM was successfully applied in ultrasensitive fluorescence detection and sensitive intracellular imaging of miRNA-21. Consequently, our strategy, based on the creation of dual-layer 3D DNA nanostructure, may create a new approach to designing the next generation of DNA nanomachine and has enormous potential for applications in bio-analysis, logic gate operations, and clinical diagnoses.
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Affiliation(s)
- Rui Meng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xiaolong Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Jiali Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ying Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Pu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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12
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Hou TL, Zhang XL, Zhou J, Chai YQ, Yuan R. Near-Infrared-Driven Nanorocket for Rapid and Ultrasensitive Detection of MicroRNA. Anal Chem 2023; 95:13156-13162. [PMID: 37606955 DOI: 10.1021/acs.analchem.3c01962] [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: 08/23/2023]
Abstract
Herein, by introducing gold nanostars (AuNSs) as fuel core, a near-infrared-driven nanorocket (NIDNR) with pretty fast walking was exploited for ultrasensitive miRNA detection. Compared with traditional nanomaterials-comprised nanomachines (NMs), the NIDNR possesses much better kinetic and thermodynamic performance owing to the extra photothermal driving force from localized surface plasmon (LSP). Impressively, the whole reaction time of NIDNR down to 15 min was realized, which is almost more than 8 times beyond those of conventional DNA-based NMs. This way, the inherent obstacle of traditional NMs, including long reaction time and low efficiency, could be easily addressed. As a proof of concept, the NIDNR was successfully applied to develop an electrochemical biosensing platform for rapid and sensitive detection of miRNA with an LOD down to 2.95 aM and achieved the real-time assay of real biological samples from human hepatocellular carcinoma cells (MHCC97L) and HeLa, thus providing an innovative insight to design more versatile DNA nanomachines for ultimate application in biosensing platform construction and clinical sample detection.
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Affiliation(s)
- Tong-Lin Hou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jie Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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13
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Su J, Sun C, Du J, Xing X, Wang F, Dong H. RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy. Adv Healthc Mater 2023; 12:e2300367. [PMID: 37084038 DOI: 10.1002/adhm.202300367] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Indexed: 04/22/2023]
Abstract
Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.
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Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Fang Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
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14
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Han Y, Zhou J, Liu F, Ouyang Y, Yuan R, Chai YQ. pH-Stimulated Self-Locked DNA Nanostructure for the Effective Discrimination of Cancer Cells and Simultaneous Detection and Imaging of Endogenous Dual-MicroRNAs. Anal Chem 2023; 95:12754-12760. [PMID: 37590171 DOI: 10.1021/acs.analchem.3c01470] [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: 08/19/2023]
Abstract
In this study, a pH-stimulated self-locked DNA nanostructure (SLDN) was developed to efficiently distinguish cancer cells from other cells for the simultaneous detection and imaging of endogenous dual-microRNAs (miRNAs). Impressively, the SLDN was specifically unlocked in the acidic environment of cancer cells to form unlocked-SLDN to disengage the i-motif sequence with a labeled fluorophore for the recovery of a fluorescence signal, resulting in the differentiation of cancer cells from normal cells. Meanwhile, unlocked-SLDN could combine and recognize the targets miRNA-21 and miRNA-155 simultaneously to trigger the hybridization chain reaction (HCR) amplification for sensitive dual-miRNA detection, with detection limits of 1.46 pM for miRNA-21 and 0.72 pM for miRNA-155. Significantly, compared with the current miRNA imaging strategy based on the traditional DNA nanostructure, the strategy proposed here remarkably eliminates the interference of normal cells to achieve high-resolution colocation imaging of miRNAs in tumor cells with an ultralow background signal. This work provided a specific differentiation method for tumor cells to materialize sensitive biomarker detection and distinguishable high-definition live-cell imaging for precise cancer diagnosis and multifactor research of tumor progression.
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Affiliation(s)
- Yichen Han
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jie Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Fang Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yu Ouyang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
- The Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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15
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Lai X, Zhao X, Peng Y, Zhang R, Pang H, Gao Z, Li D, Cao P, Pu Q, Qiao B, Pei H, Wu Q. A specific and low background nucleic acids sensing strategy based on rolling circle amplification coupled with a magnetic DNA machine. Chem Commun (Camb) 2023; 59:10153-10156. [PMID: 37530562 DOI: 10.1039/d3cc02838k] [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: 08/03/2023]
Abstract
We propose a universal fluorescence method for detection of nucleic acids based on rolling circle amplification (RCA) combined with a magnetic DNA machine and using dengue virus nucleic acids as an example target. RCA specifically amplifies the target and yields a large number of initiators employing heat-labile double-stranded DNase. The magnetic DNA machine produces a fluorescence signal and eliminates background noise. This method achieved a wide linear range, promising recovery and ultrahigh recognition specificity for one-base mismatches, and indicates the potential application of this sensing strategy in the clinical diagnosis of nucleic acids of pathogens.
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Affiliation(s)
- Xiangde Lai
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Xuan Zhao
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Yanan Peng
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Rui Zhang
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Huajie Pang
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Zhijun Gao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Dongxia Li
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Peipei Cao
- School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou 571199, China
| | - Qiumei Pu
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Bin Qiao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
- Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou 571199, China
| | - Hua Pei
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
| | - Qiang Wu
- The First Affiliated Hospital, Hainan Medical University, Haikou 570102, China.
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou 570311, China.
- Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou 571199, China
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16
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Ou X, Wan Z, Xiong Y, Huang K, Wei Z, Nuermaimaiti Z, Chen Y, Yiliya D, Lin H, Dai Z, Li Y, Chen P. Homogeneous Dual Fluorescence Count of CD4 in Clinical HIV-Positive Samples via Parallel Catalytic Hairpin Assembly and Multiple Recognitions. ACS APPLIED MATERIALS & INTERFACES 2023; 15:38285-38293. [PMID: 37526600 DOI: 10.1021/acsami.3c06742] [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: 08/02/2023]
Abstract
Regularly measuring the level of CD4+ cells is necessary for monitoring progression and predicting prognosis in patients suffering from an infection with the human immunodeficiency virus (HIV). However, the current flow cytometry standard detection method is expensive and complicated. A parallel catalytic hairpin assembly (CHA)-assisted fluorescent aptasensor is reported for homogeneous CD4 count by targeting the CD4 protein expressed on the membrane of CD4+ cells. Detection was achieved using CdTe quantum dots (QDs) and methylene blue (MB) as signal reporters. CdTe QDs distinguished CHA-assisted release of Ag+ and C-Ag+-C and MB that has differentiated cytosine (C)-rich single-stranded DNA (ssDNA) and C-Ag+-C, generating changes in fluorescence intensity. With the assistance of the CHA strategy and luminescent nanomaterials, this method reached limits of detection of 0.03 fg/mL for the CD4 protein and 0.3 cells/mL for CD4+ cells with linear ranges of 0.1 to 100 fg/mL and 1 to 1000 cells/mL, respectively. The method was validated in 50 clinical whole blood samples consisting of 30 HIV-positive patients, 10 healthy volunteers, and 10 patients with cancer or other chronic infections. The findings from this method were in good agreement with the data from clinical flow cytometry. Due to its sensitivity, affordability, and ease of operation, the current method has demonstrated great potential for routine CD4 counts for the management of HIV, especially in communities and remote areas.
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Affiliation(s)
- Xiaoqi Ou
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhengli Wan
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ying Xiong
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ke Huang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Zeliang Wei
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zulimire Nuermaimaiti
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanting Chen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Duerdanna Yiliya
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongyin Lin
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhenjie Dai
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Li
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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17
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Li XQ, Jia YL, Zhang YW, Chen HY, Xu JJ. Intracellular activated logic nanomachines based on framework nucleic acids for low background detection of microRNAs in living cells. Chem Sci 2023; 14:7699-7708. [PMID: 37484658 PMCID: PMC10356544 DOI: 10.1039/d3sc01162c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/18/2023] [Indexed: 07/25/2023] Open
Abstract
DNA molecular machines based on DNA logic circuits show unparalleled potential in precision medicine. However, delivering DNA nanomachines into real biological systems and ensuring that they perform functions specifically, quickly and logically remain a challenge. Here, we developed an efficient DNA molecular machine integrating transfer-sensor-computation-output functions to achieve high fidelity detection of intracellular biomolecules. The introduction of pH nanoswitches enabled the nanomachines to be activated after entering the cell, and the spatial-confinement effect of the DNA triangular prism (TP) enables the molecular machine to process complex information at the nanoscale, with higher sensitivity and shorter response time than diffuse-dominated logic circuits. Such cascaded activation molecular machines follow the logic of AND to achieve specific capture and detection of biomolecules in living cells through a multi-hierarchical response, providing a new insight into the construction of efficient DNA molecular machines.
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Affiliation(s)
- Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yi-Lei Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
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18
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Yang C, Shi Y, Zhang Y, He J, Li M, Huang W, Yuan R, Xu W. Modular DNA Tetrahedron Nanomachine-Guided Dual-Responsive Hybridization Chain Reactions for Discernible Bivariate Assay and Cell Imaging. Anal Chem 2023. [PMID: 37365899 DOI: 10.1021/acs.analchem.3c01091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Engineering of multivariate biosensing and imaging platforms involved in disease plays a vital role in effectively discerning cancer cells from normal cells and facilitating reliable targeted therapy. Multiple biomarkers such as mucin 1 (MUC1) and nucleolin are typically overexpressed in breast cancer cells compared to normal human breast epithelium cells. Motivated by this knowledge, a dual-responsive DNA tetrahedron nanomachine (drDT-NM) is constructed through immobilizing two recognition modules, MUC1 aptamer (MA) and a hairpin H1* encoding nucleolin-specific G-rich AS1411 aptamer, in two separate vertexes of a functional DT architecture tethering two localized pendants (PM and PN). When drDT-NM identifiably binds bivariate MUC1 and nucleolin, two independent hybridization chain reactions (HCRM and HCRN) as amplification modules are initiated with two sets of four functional hairpin reactants. Among them, one hairpin for HCRM is dually ended by fluorescein and quencher BHQ1 to sense MUC1. The responsiveness of nucleolin is executed by operating HCRN utilizing another two hairpins programmed with two pairs of AS1411 splits. In the shared HCRN duplex products, the parent AS1411 aptamers are cooperatively merged and folded into G-quadruplex concatemers to embed Zn-protoporphyrin IX (ZnPPIX/G4) for fluorescence signaling readout, thereby achieving a highly sensitive intracellular assay and discernible cell imaging. The tandem ZnPPIX/G4 unities also act as imaging agents and therapeutic cargos for efficient photodynamic therapy of cancer cells. Based on drDT-NM to guide bispecific HCR amplifiers for adaptive bivariate detection, we present a paradigm of exquisitely integrating modular DNA nanostructures with nonenzymatic nucleic acid amplification, thus creating a versatile biosensing platform as a promising candidate for accurate assay, discernible cell imaging, and targeted therapy.
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Affiliation(s)
- Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yanan Shi
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yuqing Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Mengdie Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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19
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Peng Y, Gao Z, Qiao B, Li D, Pang H, Lai X, Pu Q, Zhang R, Zhao X, Zhao G, Xu D, Wang Y, Ji Y, Pei H, Wu Q. Size-Controlled DNA Tile Self-Assembly Nanostructures Through Caveolae-Mediated Endocytosis for Signal-Amplified Imaging of MicroRNAs in Living Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2300614. [PMID: 37189216 PMCID: PMC10375201 DOI: 10.1002/advs.202300614] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/30/2023] [Indexed: 05/17/2023]
Abstract
Signal-amplified imaging of microRNAs (miRNAs) is a promising strategy at the single-cell level because liquid biopsy fails to reflect real-time dynamic miRNA levels. However, the internalization pathways for available conventional vectors predominantly involve endo-lysosomes, showing nonideal cytoplasmic delivery efficiency. In this study, size-controlled 9-tile nanoarrays are designed and constructed by integrating catalytic hairpin assembly (CHA) with DNA tile self-assembly technology to achieve caveolae-mediated endocytosis for the amplified imaging of miRNAs in a complex intracellular environment. Compared with classical CHA, the 9-tile nanoarrays possess high sensitivity and specificity for miRNAs, achieve excellent internalization efficiency by caveolar endocytosis, bypassing lysosomal traps, and exhibit more powerful signal-amplified imaging of intracellular miRNAs. Because of their excellent safety, physiological stability, and highly efficient cytoplasmic delivery, the 9-tile nanoarrays can realize real-time amplified monitoring of miRNAs in various tumor and identical cells of different periods, and imaging effects are consistent with the actual expression levels of miRNAs, ultimately demonstrating their feasibility and capacity. This strategy provides a high-potential delivery pathway for cell imaging and targeted delivery, simultaneously offering a meaningful reference for the application of DNA tile self-assembly technology in relevant fundamental research and medical diagnostics.
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Affiliation(s)
- Yanan Peng
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Zhijun Gao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Bin Qiao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, P. R. China
| | - Dongxia Li
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Huajie Pang
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Xiangde Lai
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Qiumei Pu
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Rui Zhang
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Xuan Zhao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Guangyuan Zhao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Dan Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, 571199, P. R. China
| | - Yuanyuan Wang
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, P. R. China
| | - Yuxiang Ji
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Hua Pei
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
| | - Qiang Wu
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 571199, P. R. China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, P. R. China
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Du S, Xie B, Gao H, Zhang J, Fu H, Liao F, Liao Y. Self-Powered DNAzyme Walker Enables Dual-Mode Biosensor Construction for Electrochemiluminescence and Electrochemical Detection of MicroRNA. Anal Chem 2023; 95:7006-7013. [PMID: 37083199 DOI: 10.1021/acs.analchem.3c00546] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Herein, an electrochemiluminescence (ECL) and electrochemical (EC) dual-mode biosensor platform with a self-powered DNAzyme walking machine was established for accurate and sensitive detection of miRNA-21. By employing a magnesium ion (Mn2+)-dependent DNAzyme cleavage cycling reaction, the walking machine was built by assembling DNAzyme walking strands and ferrocene (Fc)-labeled substrate strands on the Au nanoparticles and graphitic carbon nitride nanosheet (g-C3N4 NS)-covered electrode. The DNAzyme walking strand was first prohibited by a blocker strand. After the addition of target miRNA-21 and Mn2+, the DNAzyme walker could be activated and produce autonomous movements along the electrode track fueled by Mn2+-dependent DNAzyme-catalyzed substrate cleavage without additional energy supply. Notably, each walking step resulted in the cleavage of a substrate strand and the release of a Fc-labeled DNA strand fragment, allowing us to acquire an extreme ECL signal recovery of g-C3N4 inhibited by Fc. Meanwhile, numerous Fc-labeled DNA fragments escaped from the surface of the electrode, directly producing an obvious decrease in the square wave voltammetry (SWV) signal from Fc on the same sensing platform. This work not only avoided difficultly assembling various signal indicators but also significantly improved the sensitivity through using self-powered DNAzyme-walker amplification. Moreover, the proposed design employed the same reaction to produce two signal output modes, which could eliminate the interference from diverse reactive pathways on the outcome to mutually improve the accuracy. Therefore, the dual-mode miRNA-21 biosensor exhibited wide detection ranges of 100 aM to 100 nM with low detection limits of 54.3 and 78.6 aM by ECL and SWV modes, respectively, which provided an efficient and universal biosensing approach with extensive applications in early disease diagnosis and bioanalysis.
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Affiliation(s)
- Shimao Du
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Benting Xie
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Hejun Gao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Juan Zhang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Hongquan Fu
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Fang Liao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
| | - Yunwen Liao
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong, Sichuan 637000, China
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21
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Huang W, Yang C, Gao J, Ye J, Yuan R, Xu W. Cooperative Amplification of Au@FeCo as Mimetic Catalytic Nanozymes and Bicycled Hairpin Assembly for Ultrasensitive Electrochemical Biosensing. Anal Chem 2023; 95:5710-5718. [PMID: 36941819 DOI: 10.1021/acs.analchem.2c05725] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Exploring the cooperative amplification of peroxidase-like metal nanocomposites and cycled hairpin assembly is intriguing for sensitive bioanalysis. Herein, we report the first design of a unique electrochemical biosensor based on mimicking Au@FeCo nanozymes and bicycled hairpin assembly (BHA) for synergistic signal amplification. By loading the enzyme-like FeCo alloy in Au nanoparticles (AuNPs), the as-synthesized Au@FeCo hybrids display great improvement of electronic conductivity and active surface area and excellent mimic catalase activity to H2O2 decomposition into •OH radicals. The immobilization of Au@FeCo in an electrode sensing interface is stabilized via the resulting electrodeposition in HAuCl4 while efficiently accelerating the electron transfer of electroactive ferrocene (Fc). Upon the immobilization of a helping hairpin (HH) via Au-S bonds, a specific DNA trigger (T*) is introduced to activate BHA operation through competitive strand displacement reactions among recognizing hairpin (RH), signaling hairpin (SH), and HH. T* and RH are rationally released to catalyze two cycles, in which the transient depletion of dsDNA intermediates rapidly drives the progressive hairpin assemblies to output more products SH·HH. Thus, the efficient amplification of Au@FeCo mimic catalase activity combined with BHA leads to a significantly increased current signal of Fc dependent on miRNA-21 analogous to T*, thereby directing the creation of a highly sensitive electrochemical biosensor having applicable potential in actual samples.
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Affiliation(s)
- Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chunli Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jiaxi Gao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jingjing Ye
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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22
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Zhang XL, Li SS, Liu YJ, Liu WW, Kong LQ, Chai YQ, Luo XL, Yuan R. High-Efficiency 3D DNA Walker Immobilized by a DNA Tetrahedral Nanostructure for Fast and Ultrasensitive Electrochemical Detection of MiRNA. Anal Chem 2023; 95:4077-4085. [PMID: 36787389 DOI: 10.1021/acs.analchem.2c04847] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Herein, by directly limiting the reaction space, an ingenious three-dimensional (3D) DNA walker (IDW) with high walking efficiency is developed for rapid and sensitive detection of miRNA. Compared with the traditional DNA walker, the IDW immobilized by the DNA tetrahedral nanostructure (DTN) brings stronger kinetic and thermodynamic favorability resulting from its improved local concentration and space confinement effect, accompanied by a quite faster reaction speed and much better walking efficiency. Once traces of target miRNA-21 react with the prelocked IDW, the IDW could be largely activated and walk on the interface of the electrode to trigger the cleavage of H2 with the assistance of Mg2+, resulting in the release of amounts of methylene blue (MB) labeled on H2 from the electrode surface and the obvious decrease of the electrode signal. Impressively, the IDW reveals a conversion efficiency as high as 9.33 × 108 in 30 min with a much fast reaction speed, which is at least five times beyond that of typical DNA walkers. Therefore, the IDW could address the inherent challenges of the traditional DNA walker easily: slow walking speed and low efficiency. Notably, the IDW as a DNA nanomachine was utilized to construct a sensitive sensing platform for rapid miRNA-21 detection with a limit of detection (LOD) of 19.8 aM and realize the highly sensitive assay of biomarker miRNA-21 in the total RNA lysates of cancer cell. The strategy thus helps in the design of a versatile nucleic acid conversion and signal amplification approach for practical applications in the areas of biosensing assay, DNA nanotechnology, and clinical diagnosis.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Sha-Sha Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yi-Jia Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wei-Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xi-Liang Luo
- Key Laboratory of Sensor Analysis of Tumor Markers, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266061, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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23
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Liu H, Chen Y, Ju H. Functional DNA structures for cytosensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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24
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Lu Z, Ni W, Liu N, Jin D, Li T, Li K, Zhang Y, Yao Q, Zhang GJ. CRISPR/Cas12a-based fluorescence biosensor for detection of exosomal miR-21 derived from lung cancer. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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25
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Wang M, Shan L, Kong X, Pan R, Wang H, Zhou J, Ming J. A label-free fluorescence strategy for analysis of aflatoxin M1 by self-protected DNAzyme and aptamer recognition triggered DNA walker cascade amplification. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Zhang XL, Li SS, Liu WW, Kong LQ, Chai YQ, Yuan R. Programmable mismatch-fueled high-efficiency DNA signal amplifier. Chem Sci 2022; 13:11926-11935. [PMID: 36320909 PMCID: PMC9580486 DOI: 10.1039/d2sc04814k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/23/2022] [Indexed: 08/11/2023] Open
Abstract
Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Sha-Sha Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Wei-Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
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Jin Y, Wu Z, Li L, Yan R, Zhu J, Wen W, Zhang X, Wang S. Zinc-Air Battery-Based Self-Powered Sensor with High Output Power for Ultrasensitive MicroRNA let-7a Detection in Cancer Cells. Anal Chem 2022; 94:14368-14376. [PMID: 36199273 DOI: 10.1021/acs.analchem.2c03093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-powered sensors do not require a power supply and are easy to miniaturize, which have potential for constructing wearable, portable, and real-time detection devices. However, it is challenging for the detection of low abundant targets due to the low output power density of fuel cells and much interference of complex biological environment. Herein, a new kind of photocatalytic zinc-air battery-based self-powered electrochemical sensor (ZAB-SPES) was constructed for the detection of microRNA let-7a (miRNA let-7a) by combining magnetic nanobeads (MBs) with a metal-organic framework loaded with glucose oxidase (MOFs@GOX). Poly(1,4-di(2-thienyl))benzene (PDTB) was used as the photocathode material, and the proposed ZAB-SPES had a high power density of 22.8 μW/cm2, which was 2-3-fold of commonly used photofuel cells. MBs can capture and separate miRNA from complex samples quickly with a high separation efficiency of 99% within 60 s. The competitive reaction of oxygen reduction reaction between PDTB and MOFs@GOX would change the output power density of the ZAB-SPES. Based on the relationship between output power density and target concentration, the ZAB-SPES realized ultrasensitive detection of miRNA let-7a with a detection limit down to 1.38 fM. Furthermore, the successful detection of miRNA let-7a in A549 cancer cells indicated the great prospects of ZAB-SPES in clinical analysis and early diagnosis of cancers.
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Affiliation(s)
- Yunxia Jin
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Zhen Wu
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Li Li
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Ruiqiang Yan
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Junlun Zhu
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Wei Wen
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules and College of Chemistry and Chemical Engineering, Hubei University, Wuhan430062, People's Republic of China
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28
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Kang Q, Chen B, He M, Hu B. Simple Amplifier Coupled with a Lanthanide Labeling Strategy for Multiplexed and Specific Quantification of MicroRNAs. Anal Chem 2022; 94:12934-12941. [PMID: 36070565 DOI: 10.1021/acs.analchem.2c03234] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inductively coupled plasma-mass spectrometry (ICP-MS) with elemental labeling is a promising strategy for multiplex microRNA (miRNA) analysis. However, it is still challenging for specific analysis of multiple miRNAs with high homology, and the development of multiplex assays is always limited by the complexity of the sequence design. Herein, a simple and direct ICP-MS-based assay was developed for the simultaneous detection of three miRNAs by combining the lanthanide labeling strategy with entropy-driven catalytic (EDC) amplification. Owing to the specificity of EDC for nucleic acid recognition, it is able to differentiate miRNAs with single-base mutation in each EDC circuit. A universal biotin-labeled DNA strand was designed to hybridize with the DNA substrates for three EDC circuits, targeting miRNA-21, miRNA-155, and miRNA-10b, respectively. All the substrates were loaded on the surface of streptavidin magnetic beads. In the presence of target miRNA, the EDC reaction was initiated, and EDC substrates were dissociated, continuously releasing reporter strands that were labeled with lanthanides (Tb/Ho/Lu). After magnetic separation, the supernatant containing the released reporter strands was introduced into an ICP-MS system for simultaneous detection of 159Tb/165Ho/175Lu and quantification of miRNA-21, miRNA-155, and miRNA-10b, respectively. The limits of detection were 7.4, 7.5, and 11 pmol L-1 for miRNA-21, miRNA-155, and miRNA-10b, respectively. Overall, this study provides a powerful strategy for simultaneous quantification of multiple miRNAs, with the advantages of flexible probe design, good sensitivity, and excellent specificity.
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Affiliation(s)
- Qi Kang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Beibei Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Man He
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bin Hu
- Department of Chemistry, Wuhan University, Wuhan 430072, China
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29
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Wang Y, Zhao P, Zhang S, Zhu K, Shangguan X, Liu L, Zhang S. Application of Janus Particles in Point-of-Care Testing. BIOSENSORS 2022; 12:bios12090689. [PMID: 36140074 PMCID: PMC9496037 DOI: 10.3390/bios12090689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 06/01/2023]
Abstract
Janus particles (JPs), named after the two-faced Roman god, are asymmetric particles with different chemical properties or polarities. JPs have been widely used in the biomedical field in recent years, including as drug carriers for targeted controlled drug release and as biosensors for biological imaging and biomarker detection, which is crucial in the early detection and treatment of diseases. In this review, we highlight the most recent advancements made with regard to Janus particles in point-of-care testing (POCT). Firstly, we introduce several commonly used methods for preparing Janus particles. Secondly, we present biomarker detection using JPs based on various detection methods to achieve the goal of POCT. Finally, we discuss the challenges and opportunities for developing Janus particles in POCT. This review will facilitate the development of POCT biosensing devices based on the unique properties of Janus particles.
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30
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Hou TL, Zhu L, Zhang XL, Chai YQ, Yuan R. Multiregion Linear DNA Walker-Mediated Ultrasensitive Electrochemical Biosensor for miRNA Detection. Anal Chem 2022; 94:10524-10530. [PMID: 35822933 DOI: 10.1021/acs.analchem.2c02004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, an intelligent multiregion linear DNA walker (MLDW) with a high walking rate and a high amplification efficiency was explored for ultrasensitive detection of miRNA. Significantly, amounts of functional domain could be concentrated in a long linear DNA obtained by the target miRNA-mediated rolling-circle amplification to simultaneously increase the local concentration and collision probability, resulting in an obviously improved reaction rate. Impressively, the MLDW can accomplish the reaction within 30 min, which is at least 4 times beyond that of traditional single-leg and multiple-leg DNA walkers. As a proof of concept, the high-efficiency MLDW was used to develop an electrochemical biosensing platform for ultrasensitive detection of target miRNA-21 with a low detection limit down to 36 aM. Therefore, the MLDW we designed puts forward an innovative insight to construct a functional DNA nanodevice and promote the investigation of the inherent performance of nucleic acid signal amplification for ultimate application in the detection of biomolecules and clinical disease diagnosis.
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Affiliation(s)
- Tong-Lin Hou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Liang Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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31
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Zhou J, Peng X, Yang Z, Zhuo Y, Liang W, Yuan R, Chai Y. Discrimination between Cancer Cells and DNA-Damaged Cells: Pre-miRNA Region Recognition Based on Hyperbranched Hybrid Chain Reaction Amplification for Simultaneous Sensitive Detection and Imaging of miRNA and Pre-miRNA. Anal Chem 2022; 94:9911-9918. [PMID: 35749657 DOI: 10.1021/acs.analchem.2c01918] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Herein, a novel region recognition of precursor microRNA (Pre-miRNA) based on hyperbranched hybrid chain reaction (HB-HCR) amplification was constructed to effectively eliminate the interference of Pre-miRNA to the mature microRNA (miRNA) by establishing the linear mapping relation between the two fluorescence signals produced by the miRNA sequence in the Pre-miRNA and Pre-miRNA residues to first realize simultaneous sensitive detection of Pre-miRNA and miRNA as well as highly sensitive imaging of intracellular Pre-miRNA and miRNA, which solves one main challenge of in vitro tumor disease diagnostics: inaccurate detection of tumor-induced miRNA changes. Impressively, this strategy easily distinguishes cancer cells from normal cells and DNA-damaged cells by the difference in miRNA and Pre-miRNA expression, which provides an innovative approach for accurate clinical diagnosis of cancer and precise treatment of prognosis.
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Affiliation(s)
- Jie Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Xin Peng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zezhou Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenbin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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Zhao Y, Lu C, Zhao XE, Kong W, Zhu S, Qu F. A T-rich nucleic acid-enhanced electrochemical platform based on electroactive silver nanoclusters for miRNA detection. Biosens Bioelectron 2022; 208:114215. [DOI: 10.1016/j.bios.2022.114215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022]
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Tian Z, Zhou C, Zhang C, Wu M, Duan Y, Li Y. Recent advances of catalytic hairpin assembly and its application in bioimaging and biomedicine. J Mater Chem B 2022; 10:5303-5322. [PMID: 35766024 DOI: 10.1039/d2tb00815g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic hairpin assembly (CHA) appears to be a particularly appealing nucleic acid circuit because of its powerful amplification capability, simple protocols, and enzyme-free and isothermal conditions, and can combine with various signal output modes for the biosensing of various analytes. Especially in the last five years, vast CHA related studies have sprung up. With the deep exploration of the CHA mechanism, some novel and excellent CHA strategies have been proposed; meanwhile the CHA cascade strategies with various amplification techniques further improve the analysis performance. Furthermore, diverse CHA based biosensors have been tactfully engineered and extensively employed in imaging applications in living cells and in vivo ascribed to its gentle reaction, efficient amplification and universality. Hence, we present a comprehensive and systematic summary of the progress in CHA and its application in bioimaging and biomedicine to date. At first, we introduced the mechanism and diversification of CHA in detail, including the newly developed CHA and its ingenious combination with a variety of other technologies. Concurrently, we summarized the latest application progress of different CHA strategies in bioimaging and biomedicine, highlighting the merits and drawbacks of representative approaches. Finally, we put forward some views on the challenges and prospects of CHA in bioimaging and biomedicine in the future.
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Affiliation(s)
- Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Chen Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Chuyan Zhang
- 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.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
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Chen Y, Meng X, Lu H, Dong H. Engineering DNA walkers for bioanalysis: A review. Anal Chim Acta 2022; 1209:339339. [PMID: 35569865 DOI: 10.1016/j.aca.2021.339339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/19/2022]
Abstract
Considerable advances have been made in the design, modularization, functionalization, and regulation of DNA nanostructures over the past 40 years. These advances have accelerated the development of DNA nanomachines such as DNA walkers, dynamic nanomachines with walking feet, tracks, and driven forces, which have highly sensitive detection and signal amplification abilities that can be applied to various bioanalytical contexts and therapeutic strategies. Here, we describe a rational design of the nano-bio interface, the kinetics of DNA walkers and the strategies for improving their efficiency and sensitivity. We also outline the various bioanalytic and imaging applications to which DNA walkers have been applied, such as electrochemical and optical measurements, when integrated with other simulation and activation tools. Finally, we compare the performances of novel DNA walker-based strategies for bioanalysis and propose a method to improve DNA walker design.
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Affiliation(s)
- Yuchao Chen
- Research Center for Bioengineering and Sensing Technology, School of Chemical and Bioengineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiangdan Meng
- Research Center for Bioengineering and Sensing Technology, School of Chemical and Bioengineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China.
| | - Huiting Lu
- Department of Chemistry, School of Chemistry and Bioengineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China.
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, School of Chemical and Bioengineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China; Marshall Laboratory of Biomedical Engineering, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, 518071, China.
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35
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Proximity hybridization-induced competitive rolling circle amplification to construct fluorescent dual-sensor for simultaneous evaluation of glycated and total hemoglobin. Biosens Bioelectron 2022; 202:113998. [DOI: 10.1016/j.bios.2022.113998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 11/18/2022]
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Wang DD, Zhang J, Yu QQ, Zhang K, Chen TT, Chu X. Biomineralized Zeolitic Imidazolate Framework-8 Nanoparticles Enable Polymerase-Driven DNA Biocomputing for Reliable Cell Identification. Anal Chem 2022; 94:4794-4802. [PMID: 35266710 DOI: 10.1021/acs.analchem.1c05605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Investigating multiple miRNA expression patterns in living cells by DNA logic biocomputing is a valuable strategy for diagnosis and biomedical studies. The introduction of protein enzymes in DNA logic biocomputing circuits not only expands the toolbox of nucleic acid assembly techniques, but also further improves the specificity of recognizing and processing of DNA input. Herein, a polymerase-driven primer exchange reaction, acting as the sensing module, is introduced into the biocomputing system and transduces the multiple miRNAs sensing event into the intermediate triggers for activating the subsequent processing module, which further performs signal readout through DNAzyme catalytic substrate cleavage reaction. By using biomineralized zeolitic imidazolate framework-8 nanoparticles (ZIF-8 NPs) to deliver all the components of the biocomputing system, including polymerase and DNA probes, we realized polymerase-driven DNA biocomputing operations in living cells, including AND and OR gates. The results exhibited that biomineralized ZIF-8 NPs can protect the loaded cargoes against the external environment and deliver them efficiently to the cytoplasm. The polymerase-driven DNA biocomputing system based on multiple miRNAs sensing can be used for reliable cell identification and may provide a promising platform for more accurate diagnosis and programmable therapeutics.
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Affiliation(s)
- Dan-Dan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qiao-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ke Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ting-Ting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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37
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Li X, Chen L, Cui D, Jiang W, Han L, Niu N. Preparation and application of Janus nanoparticles: Recent development and prospects. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214318] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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38
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Liu Y, Li B, Wang YJ, Fan Z, Du Y, Li B, Liu YJ, Liu B. In Situ Single-Molecule Imaging of MicroRNAs in Switchable Migrating Cells under Biomimetic Confinement. Anal Chem 2022; 94:4030-4038. [PMID: 35213802 DOI: 10.1021/acs.analchem.1c05223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Spatial imaging of RNAs in single cells is extremely charming for deciphering of regulatory mechanisms in multiple migration modes during tumor metastasis. Herein, enzyme-free-mediated cascade amplified nanoprobes were designed for in situ single-molecule imaging of dual-microRNAs (miRNAs) in switchable migrating cells. Differential expression and localization of dual-miRNAs were clearly exhibited in multiple cell lines attributed to enhanced sensitivity via the cascade signal amplification strategy. Significantly, in situ three-dimensional (3D) imaging of dual-miRNAs in transition of cell migration phenotypes was successfully reconstructed in both non-confined and confined microenvironments in vitro, of which differential spatial distribution was observed in a single cell. This is very promising for exploring key roles of spatial RNA distribution in migrating cells at the single-molecule level, which will advance revealing the molecular mechanism and physical principle in 3D cell migration in vivo.
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Affiliation(s)
- Yixin Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Ya-Jun Wang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Zihui Fan
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Yang Du
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Bin Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Yan-Jun Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
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40
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Zhang X, Yin Y, Du S, Kong L, Yang Z, Chang Y, Chai Y, Yuan R. Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104084. [PMID: 34913619 PMCID: PMC8811820 DOI: 10.1002/advs.202104084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/08/2021] [Indexed: 05/09/2023]
Abstract
Herein, a programmable dual-catalyst hairpin assembly (DCHA) for realizing the synchronous recycle of two catalysts is developed, displaying high reaction rate and outstanding conversion efficiency beyond traditional nucleic acid signal amplifications (NASA). Once catalyst I interacts with the catalyst II, the DCHA can be triggered to realize the simultaneous recycle of catalysts I and II to keep the highly concentrated intermediate product duplex I-II instead of the steadily decreased one in typical NASA, which can accomplish in about only 16 min and achieves the outstanding conversion efficiency up to 4.54 × 108 , easily conquering the main predicaments of NASA: time-consuming and low-efficiency. As a proof of the concept, the proposed DCHA as a high-speed and hyper-efficiency DNA signal magnifier is successfully applied in the rapid and ultrasensitive detection of miRNA-21 in cancer cell lysates, which exploits the new generation of universal strategy for the applications in biosensing assay, clinic diagnose, and DNA nanobiotechnology.
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Affiliation(s)
- Xiao‐Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Yang Yin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Shu‐Min Du
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Ling‐Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Zhe‐Han Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Yuan‐Yuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Ya‐Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
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41
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Song S, Li N, Bai L, Gai P, Li F. Photo-Assisted Robust Anti-Interference Self-Powered Biosensing of MicroRNA Based on Pt-S Bonds and the Inorganic-Organic Hybridization Strategy. Anal Chem 2022; 94:1654-1660. [PMID: 35025211 DOI: 10.1021/acs.analchem.1c04135] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Photo-assisted biofuel cell-based self-powered biosensors (PBFC-SPBs) possess the advantages of no need for external power supply, ease of sensing design, and simple instruments. In this work, a robust anti-interference PBFC-SPB for microRNA detection was constructed based on the Pt-S bond and the inorganic-organic hybridization strategy. The organic semiconductor [6,6]-phenyl-C61-butyric acid methylester@anthraquinone (PCBM@anthraquinone) served as an efficient light-harvesting material, and gold nanoparticle@Pt (AuNP@Pt) nanomaterials were immobilized on the surface via electrostatic adsorption for the binding of DNA. Notably, compared to Au-S bonds for DNA immobilization, the Pt-S bond exhibited better anti-interference ability. Ingeniously, cadmium sulfide quantum dots (CdS QDs) were close to the PCBM@anthraquinone substrate electrode to form sensitization structures, which was beneficial to enhance the photocurrent signal. Combining with the laccase-mimicking activity Cu2+/carbon nanotubes (Cu2+/CNTs) cathode, the PBFC-SPB for microRNA detection was achieved. Once the target existed, the identical sequence complementary microRNA would make DNA2/CdS dissociate and break away from the electrode, leading to a low signal. The linear detection range was 10 fM-100 pM, with the limit of determination of 2.4 fM (3S/N). The as-proposed strategy not only paves a new way for the design of photoelectrochemical biosensing but also opens a door for the construction of robust anti-interference bioassay for microRNA detection.
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Affiliation(s)
- Shichao Song
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Na Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Lipeng Bai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
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42
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Chen Y, Dai W, Wang D, Dong H. A Cancer Cell Membrane Vesicle-packaged DNA Nanomachine for Intracellular microRNAs Imaging. Chem Commun (Camb) 2022; 58:9488-9491. [DOI: 10.1039/d2cc03068c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cancer cell membrane vesicle encapsulated gold nanoparticles with programmable DNA nanomachine was established. Both the homing-targeting ability and fast dynamic response were achieved for amplification analysis of microRNAs in...
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43
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Xia LY, Tang YN, Zhang J, Dong TY, Zhou RX. Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications. Semin Cancer Biol 2022; 86:1105-1119. [PMID: 34979273 DOI: 10.1016/j.semcancer.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.
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Affiliation(s)
- Ling-Ying Xia
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ya-Nan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Tian-Yu Dong
- College of Chemistry, Sichuan University Chengdu, Sichuan 610064, PR China
| | - Rong-Xing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China.
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44
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Li MJ, An SY, Wu Y. Photoelectrochemical monitoring of miRNA based on Au NPs@g-C 3N 4 coupled with exonuclease-involved target cycle amplification. Anal Chim Acta 2021; 1187:339156. [PMID: 34753579 DOI: 10.1016/j.aca.2021.339156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Herein, a sensitive photoelectrochemical (PEC) biosensing platform was designed for quantitative monitoring of microRNA-141 (miRNA-141) based on Au nanoparticles@graphitic-like carbon nitride (Au NPs@g-C3N4) as the signal generator accompanying with T7 exonuclease (T7 Exo)-involved target cycle amplification process. Initially, the prepared Au NPs@g-C3N4 as the signal generator was coated on the electrode surface, which could produce a strong PEC signal due to the unique optical and electronic properties of g-C3N4 and the surface plasmonic resonance (SPR) enhanced effect of Au NPs. Meanwhile, the modified Au NPs@g-C3N4 was also considered as the fixed platform for immobilization of S1-S2 through Au-N bond. Thereafter, the T7 Exo-involved target cycle amplification process would be initiated in existence of miRNA-141 and T7 Exo, leading to abundant single chain S1 exposed on electrode surface. Ultimately, the S3-SiO2 composite was introduced through DNA hybridization, thereby producing high steric hindrance to block external electrons supply and light harvesting, which would further cause a significantly quenched PEC signal. Experimental results revealed that the PEC signal was gradually inhibited with the raising miRNA-141 concentration in the range from 1 fM to 1 nM with a detection limit of 0.3 fM. The PEC biosensor we proposed here provides a valuable scheme in miRNA assay for early disease diagnosis and biological research.
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Affiliation(s)
- Meng-Jie Li
- School of Civil Engineering and Architecture, Chongqing University of Science & Technology, Chongqing, 401331, PR China; Institute for Health and Environment, Chongqing University of Science & Technology, Chongqing, 401331, PR China.
| | - Si-Yu An
- School of Civil Engineering and Architecture, Chongqing University of Science & Technology, Chongqing, 401331, PR China; Institute for Health and Environment, Chongqing University of Science & Technology, Chongqing, 401331, PR China
| | - Ying Wu
- School of Civil Engineering and Architecture, Chongqing University of Science & Technology, Chongqing, 401331, PR China; Institute for Health and Environment, Chongqing University of Science & Technology, Chongqing, 401331, PR China
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45
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Wu Y, Fu C, Shi W, Chen J. Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection. Talanta 2021; 235:122735. [PMID: 34517602 DOI: 10.1016/j.talanta.2021.122735] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.
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Affiliation(s)
- Yan Wu
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China.
| | - Cuicui Fu
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Wenbing Shi
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Jinyang Chen
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China.
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46
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Liu JL, Yang R, Chai YQ, Yuan R. Versatile Luminol/Dissolved Oxygen/Fe@Fe 2O 3 Nanowire Ternary Electrochemiluminescence System Combined with Highly Efficient Strand Displacement Amplification for Ultrasensitive microRNA Detection. Anal Chem 2021; 93:13334-13341. [PMID: 34553919 DOI: 10.1021/acs.analchem.1c03102] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, a versatile ECL biosensor was fabricated for ultrasensitive detection of microRNA-21 (miRNA-21) from cancer cells based on a novel H2O2-free electrochemiluminescence (ECL) system (luminol/dissolved oxygen/Fe@Fe2O3 nanowires). Compared with the previously reported coreaction accelerator that needed a negative potential to produce reactive oxygen species (ROS), these newly discovered Fe@Fe2O3 nanowires could generate ROS in the detection solution immediately without the application of voltage, which narrowed down the detection potential range to avoid side reactions, favoring their practical application in biological systems. Especially, the Fe@Fe2O3 nanowires could produce H• for activating dissolved oxygen into ROS to improve the ECL intensity dramatically, which initiates a novel pathway to promote the generation of ROS for the ECL system. In addition, an original strand displacement amplification coupled with strand displacement reaction (SDA-SDR) was developed to improve the conversion efficiency of the target for sensitive detection of miRNA-21. By virtue of the SDR, a quadruple quenching effect was achieved through each output DNA strand of SDA; hence, the nucleic acid signal amplification efficiency was effectively enhanced. As expected, on account of the superb activation performance of Fe@Fe2O3 nanowires and the outstanding amplification efficiency of the SDR-SDA strategy, the fabricated ECL biosensor realized ultrasensitive detection of miRNA-21 with a detection limit down to 52.5 aM. The established ECL sensing platform ushered a new route for H2O2-free detection and a promising biomarker assay method for clinical diagnosis.
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Affiliation(s)
- Jia-Li Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Rong Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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Ye M, Kong Y, Zhang C, Lv Y, Cheng S, Hou D, Xian Y. Near-Infrared Light Controllable DNA Walker Driven by Endogenous Adenosine Triphosphate for in Situ Spatiotemporal Imaging of Intracellular MicroRNA. ACS NANO 2021; 15:14253-14262. [PMID: 34409836 DOI: 10.1021/acsnano.1c02229] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As a powerful signal amplification tool, the DNA walker has been widely applied to detect rare microRNA (miRNA) in vivo. Despite the significant advances, a near-infrared (NIR) light controllable DNA walker for signal amplification powered by an endogenous initiator has not been realized, which is crucial for spatiotemporal imaging of miRNA in living cells with high sensitivity. Herein, we constructed a NIR-photoactivatable DNA walker system, which was powered by endogenous adenosine triphosphate (ATP) for in situ miRNA imaging with spatial and temporal resolution. The system was very stable with an extremely low fluorescent background for the bioimaging in living cells. We employed upconversion nanoparticles (UCNPs) as the carriers of the DNA probe and transducers of converting NIR to UV light. Coupled with the DNA walker fueled by intracellular ATP, a smart system based on the NIR light initiated DNA walker was successfully developed for precise spatiotemporal control in living cells. Triggered by NIR light, the DNA walker could autonomously and progressively travel along the track with the assistance of intracellular ATP. The system has been successfully applied for in situ miRNA imaging in different cell lines with highly spatial and temporal resolution. This strategy can expand NIR photocontrol the DNA walker for precise imaging in a biological system.
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Affiliation(s)
- Mingqiang Ye
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yujing Kong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Cuiling Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yifei Lv
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Shasha Cheng
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Dongyan Hou
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yuezhong Xian
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
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48
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Liu J, Yang L, Xue C, Huang G, Chen S, Zheng J, Yang R. Reductase and Light Programmatical Gated DNA Nanodevice for Spatiotemporally Controlled Imaging of Biomolecules in Subcellular Organelles under Hypoxic Conditions. ACS APPLIED MATERIALS & INTERFACES 2021; 13:33894-33904. [PMID: 34275283 DOI: 10.1021/acsami.1c08979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Monitoring hypoxia-related changes in subcellular organelles would provide deeper insights into hypoxia-related metabolic pathways, further helping us to recognize various diseases on subcellular level. However, there is still a lack of real-time, in situ, and controllable means for biosensing in subcellular organelles under hypoxic conditions. Herein, we report a reductase and light programmatical gated nanodevice via integrating light-responsive DNA probes into a hypoxia-responsive metal-organic framework for spatiotemporally controlled imaging of biomolecules in subcellular organelles under hypoxic conditions. A small-molecule-decorated strategy was applied to endow the nanodevice with the ability to target subcellular organelles. Dynamic changes of mitochondrial adenosine triphosphate under hypoxic conditions were chosen as a model physiological process. The assay was validated in living cells and tumor tissue slices obtained from mice models. Due to the highly integrated, easily accessible, and available for living cells and tissues, we envision that the concept and methodology can be further extended to monitor biomolecules in other subcellular organelles under hypoxic conditions with a spatiotemporal controllable approach.
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Affiliation(s)
- Jin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Le Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Caoye Xue
- Hunan Institute of Sports Science, 410003 Changsha, China
| | - Ge Huang
- Department of Anesthesiology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Shiya Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 Hunan, China
| | - Ronghua Yang
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410006 Hunan, China
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49
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Li X, Yang F, Gan C, Yuan R, Xiang Y. 3D DNA Scaffold-Assisted Dual Intramolecular Amplifications for Multiplexed and Sensitive MicroRNA Imaging in Living Cells. Anal Chem 2021; 93:9912-9919. [PMID: 34232629 DOI: 10.1021/acs.analchem.1c02124] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The simultaneous live-cell imaging of multiple intracellular and disease-related microRNAs (miRNAs) with low abundances is highly important to enhance specificity and accuracy for disease diagnosis. On the basis of the improved cell internalization and accelerated reaction kinetics, we develop a three-dimensional (3D) DNA nanoprobe that integrates intramolecular DNAzyme (intra-Dz) and catalytic hairpin assembly (intra-CHA) amplifications to simultaneously monitor multiple miRNAs in living cells. The sensing components are loaded on a DNA scaffold via the sticky-end hybridization of the DNA sequences to increase the local concentrations of the signal probes. The miRNA-21 and miRNA-155 target sequences can trigger intra-Dz and -CHA amplifications on the nanoprobes to show significantly amplified and distinct fluorescence at different wavelengths for simultaneously monitoring low levels of miRNAs. Real-time fluorescence microscopy reveals that such a 3D DNA nanoprobe design with the intra-Dz and -CHA amplifications can accelerate the reaction rate compared to that of the conventional free Dz and CHA because of the increased local concentrations of the sensing components. Importantly, the 3D DNA nanoprobe has desirable stability and biocompatibility and can be readily delivered into living cells to achieve multiplexed and highly sensitive sensing of intracellular miRNA-155 and miRNA-21 sequences. With the demonstration of its intracellular application, the developed 3D DNA nanoprobe thus holds promising potential for biological studies and accurate disease diagnosis.
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Affiliation(s)
- Xia Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Fang Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chunfang Gan
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials Science, Nanning Normal University, Nanning 530001, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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50
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Zhang XL, Liu YH, Du SM, Yin Y, Kong LQ, Chang YY, Chai YQ, Li ZH, Yuan R. Engineering a Rolling-Circle Strand Displacement Amplification Mediated Label-Free Ultrasensitive Electrochemical Biosensing Platform. Anal Chem 2021; 93:9568-9574. [PMID: 34210120 DOI: 10.1021/acs.analchem.1c01677] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, an original rolling-circle strand displacement amplification (RC-SDA) was developed by introducing a circle DNA with two recognition domains as a template instead of the limited liner DNA template in traditional strand displacement amplification (SDA), which displayed much shorter reaction time down to 30 min and quite higher conversion efficiency of more than 1.77 × 108 compared with those of traditional strand displacement amplification (SDA) and could be applied to construct a label-free biosensor for ultrasensitive detection of an HIV DNA fragment. Once the target HIV DNA fragment interacts with the template circle DNA, the RC-SDA could be activated to dramatically output amounts of mimic target DNA with the assistance of the Phi29 DNA polymerase and Nb.BbvCI enzyme. In application, while the output products were captured by the DNA tetrahedral nanoprobe (DTNP) modified electrode, the electrochemical tag silver nanoclusters (AgNCs) on DTNP would be released from the electrode surface, accompanied with an obviously decreased electrochemical signal. This way, the developed signal-off biosensor was successfully applied to realize the rapid and ultrasensitive detection of target HIV DNA fragment with a detection limit down to 0.21 fM, which exploits the new generation of a universal strategy beyond the traditional ones for applications in biosensing assay, clinic diagnosis, and DNA nanobiotechnology.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yu-Han Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Shu-Min Du
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yang Yin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yuan-Yuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Zhao-Hui Li
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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