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Ye J, Liang Q, Tan Q, Chai M, Cheng W, Fan M, Zhang Y, Zhan J, Wang Y, Wen J, Zhang Y, Zhao X, Zhang D. A bulged-type enzyme-free recognition strategy designed for single nucleotide polymorphisms integrating with label-free electrochemical biosensor. Biosens Bioelectron 2024; 263:116601. [PMID: 39053148 DOI: 10.1016/j.bios.2024.116601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Compared to conventional nucleic acid detection methods, label-free single nucleotide polymorphism (SNP) detection presents challenging due to the necessity of discerning single base mismatches, especially in the field of enzyme-free detection. In this study, we introduce a novel bulged-type DNA duplex probe designed to significantly amplify single-base differences. This probe is integrated with programmable DNA-based nanostructures to develop a sensitive, label-free biosensor for nonenzymatic SNP detection. The duplex probe with one bulge could selectively identify wild-typed DNA (WT) and mutant-type DNA (MT) based on a competitive strand displacement reaction mechanism. The hyperbranched HCR (HHCR) by incorporating of hairpin DNA into the DNA tetrahedron and surface-tethering on the portable screen printing electrode (SPCE) significantly favor the formation of negatively charged DNA nanostructure. We harnessed strong repulsion of DNA nanostructure towards the electroactive [Fe(CN)₆]³⁻/⁴⁻ in combination with electrochemical technique to create a label-free biosensor. This simple, enzyme-free and label-free biosensor could detect MT with a detection limit of 56 aM, even in multiple sequence backgrounds. The study served as the proof-of-concept for the integration of enzyme-free competitive mechanism and label-free strategy, which can be extended as a powerful tool to various fields.
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Affiliation(s)
- Jing Ye
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Qi Liang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Qianglong Tan
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Mengyao Chai
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Wendai Cheng
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Minzhi Fan
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Yunshan Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Jie Zhan
- New Materials Computing Center, Zhejiang Laboratory, Hangzhou, 311121, China
| | - Yaxin Wang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Jiahong Wen
- The College of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Yongjun Zhang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Xiaoyu Zhao
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Diming Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou, 311121, China.
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2
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Li XY, Zhou BX, Xiao YL, Liu X, Wang YQ, Li MM, Wang JP. Label-free and ultrasensitive detection of environmental lead ions based on spatially localized DNA nanomachines driven by hyperbranched hybridization chain reaction. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135115. [PMID: 38976962 DOI: 10.1016/j.jhazmat.2024.135115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/23/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
A label-free fluorescent sensing strategy for the rapid and highly sensitive detection of Pb2+ was developed by integrating Pb2+ DNAzyme-specific cleavage activity and a tetrahedral DNA nanostructure (TDN)-enhanced hyperbranched hybridization chain reaction (hHCR). This strategy provides accelerated reaction rates because of the highly effective collision probability and enriched local concentrations from the spatial confinement of the TDN, thus showing a higher detection sensitivity and a more rapid detection process. Moreover, a hairpin probe based on a G-triplex instead of a G-quadruplex or chemical modification makes hybridization chain reaction more controlled and flexible, greatly improving signal amplification capacities and eliminating labeled DNA probes. The enhanced reaction rates and improved signal amplification efficiency endowed the biosensors with high sensitivity and a rapid response. The label-free detection of Pb2+ based on G-triplex combined with thioflavin T can be achieved with a detection limit as low as 1.8 pM in 25 min. The proposed Pb2+-sensing platform was also demonstrated to be applicable for Pb2+ detection in tap water, river water, shrimp, rice, and soil samples, thus showing great potential for food safety and environmental monitoring.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety (Ministry of Education), College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Bo-Xi Zhou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety (Ministry of Education), College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yu-Ling Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety (Ministry of Education), College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Xin Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety (Ministry of Education), College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Yong-Qian Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety (Ministry of Education), College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Ming-Min Li
- Life and Health Research Institute School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, PR China
| | - Jun-Ping Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety (Ministry of Education), College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China.
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3
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Li M, Luo H, Wang Z, Mo Q, Zhong S, Mao YA, Li S, Li X. Tuning quantum dots emission on DNA tetrahedron/silica nanosphere/graphene oxide nanointerface for ratiometric fluorescence assay of Pb 2+ in multiplex samples. Anal Chim Acta 2024; 1310:342716. [PMID: 38811135 DOI: 10.1016/j.aca.2024.342716] [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: 09/11/2023] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Assembling framework nucleic acid (FNA) nanoarchitectures and tuning luminescent quantum dots (QDs) for fluorescence assays represent a versatile strategy in analytical territory. Rationally, FNA constructs could offer a preferential orientation to efficiently recognize the target and improve detection sensitivity, meanwhile, regulating size-dependent multicolor emissions of QDs in one analytical setting for ratiometric fluorescence assay would greatly simplify operation procedures. Nonetheless, such FNA/QDs-based ratiometric fluorescence nanoprobes remain rarely explored. RESULTS We designed a sensitive and signal amplification-free fluorescence aptasensor for lead ions (Pb2+) that potentially cause extensive contamination to environment, cosmetic, food and pharmaceuticals. Red and green emission CdTe quantum dots (rQDs and gQDs) were facilely prepared. Moreover, silica nanosphere encapsulating rQDs served as quantitative internal reference and scaffold to anchor a predesigned FNA and DNA sandwich containing Pb2+ binding aptamer and gQD modified DNA signal reporter. On binding of Pb2+, the gQD-DNA signal reporter was set free, resulting in fluorescence quenching at graphene oxide (GO) interface. Owing to the rigid structure of FNA, the fluorescence signal reporter orderly arranged at the silica nanosphere could sensitively respond to Pb2+ stimulation. The dose-dependent fluorescence signal-off mode enabled ratiometric analysis of Pb2+ without cumbersome signal amplification. Linear relationship was established between fluorescence intensity ratio (I555/I720) and Pb2+ concentration from 10 nM to 2 μM, with detection limit of 1.7 nM (0.43 ppb), well addressing the need for Pb2+ routine monitoring. The designed nanoprobe was applied to detection of Pb2+ in soil, cosmetic, milk, drug, and serum samples, with the sensitivity comparable to conventional ICP-MS technique. SIGNIFICANCE Given the programmable design of FNA and efficient recognition of target, flexible tuning of QDs emission, and signal amplification-free strategy, the present fluorescence nanoprobe could be a technical criterion for other heavy metal ions detection in a straightforward manner.
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Affiliation(s)
- Manting Li
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China; Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Haikun Luo
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Zhao Wang
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Qian Mo
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Shanshan Zhong
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Yu-Ang Mao
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China.
| | - Shuting Li
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Xinchun Li
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China; Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China; State Key Laboratory of Targeting Oncology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China.
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4
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Li Y, Tang X, Deng R, Feng L, Xie S, Chen M, Zheng J, Chang K. Dumbbell Dual-Hairpin Triggered DNA Nanonet Assembly for Cascade-Amplified Sensing of Exosomal MicroRNA. ACS OMEGA 2024; 9:19723-19731. [PMID: 38708273 PMCID: PMC11064005 DOI: 10.1021/acsomega.4c02652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Exosomal microRNAs (miRNAs) are valuable biomarkers closely associated with cancer progression. Therefore, sensitive and specific exosomal miRNA biosensing has been employed for cancer diagnosis, prognosis, and prediction. In this study, a miRNA-based DNA nanonet assembly strategy is proposed, enabling the biosensing of exosomal miRNAs through dumbbell dual-hairpin under isothermal enzyme-free conditions. This strategy dexterously designs a specific dumbbell dual-hairpin that can selectively recognize exosomal miRNA, inducing conformational changes to cascade-generated X-shaped DNA structures, facilitating the extension of the X-shaped DNA in three-dimensional space, ultimately forming a DNA nanonet assembly. On the basis of the target miRNA, our design enriches the fluorescence signal through the cascade assembly of DNA nanonet and realizes the secondary signal amplification. Using exosomal miR-141 as the target, the resultant fluorescence sensing demonstrates an impressive detection limit of 57.6 pM and could identify miRNA sequences with single-base variants with high specificity. Through the analysis of plasma and urine samples, this method effectively distinguishes between benign prostatic hyperplasia, prostate cancer, and metastatic prostate cancer. Serving as a novel noninvasive and accurate screening and diagnostic tool for prostate cancer, this dumbbell dual-hairpin triggered DNA nanonet assembly strategy is promising for clinical applications.
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Affiliation(s)
- Yongxing Li
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
- Department
of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), 183 Xinqiao, Shapingba
District, Chongqing 400037, P. R. China
- School
of Medicine, Chongqing University, Chongqing 400030, P. R. China
| | - Xiaoqi Tang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ruijia Deng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Liu Feng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Shuang Xie
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ming Chen
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ji Zheng
- Department
of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), 183 Xinqiao, Shapingba
District, Chongqing 400037, P. R. China
- School
of Medicine, Chongqing University, Chongqing 400030, P. R. China
| | - Kai Chang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
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5
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Wu X, Ju T, Li Z, Li J, Zhai X, Han K. Target-independent hybridization chain reaction-fluorescence resonance energy transfer for sensitive assay of ctDNA based on Cas12a. Anal Chim Acta 2023; 1261:341170. [PMID: 37147050 DOI: 10.1016/j.aca.2023.341170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 05/07/2023]
Abstract
Circulating tumor DNA (ctDNA) is a noninvasive biomarker which offer valuable information for cancer diagnosis and prognosis. In this study, a target-independent fluorescent signal system, Hybridization chain reaction-Fluorescence resonance energy transfer (HCR-FRET) system, is designed and optimized. Combined with CRISPR/Cas12a system, a fluorescent biosensing protocol was developed for sensing assay of T790 M. When the target is absent, the initiator remains intact, opens the fuel hairpins and triggers the following HCR-FRET. At presence of the target, the Cas12a/crRNA binary complex specifically recognizes the target, and the Cas12a trans-cleavage activity is activated. As a result, the initiator is cleaved and subsequent HCR responses and FRET processes are attenuated. This method showed detection range from 1 pM to 400 pM with a detection limit of 316 fM. The target independent property of the HCR-FRET system endows this protocol a promising potential to transplant to the assay of other DNA target in parallel.
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Affiliation(s)
- Xuelan Wu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Ting Ju
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Zeyang Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Jingwen Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Xingwei Zhai
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China
| | - Kun Han
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215163, China.
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6
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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7
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Li H, Zhang Z, Gan L, Fan D, Sun X, Qian Z, Liu X, Huang Y. Signal Amplification-Based Biosensors and Application in RNA Tumor Markers. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094237. [PMID: 37177441 PMCID: PMC10180857 DOI: 10.3390/s23094237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Tumor markers are important substances for assessing cancer development. In recent years, RNA tumor markers have attracted significant attention, and studies have shown that their abnormal expression of post-transcriptional regulatory genes is associated with tumor progression. Therefore, RNA tumor markers are considered as potential targets in clinical diagnosis and prognosis. Many studies show that biosensors have good application prospects in the field of medical diagnosis. The application of biosensors in RNA tumor markers is developing rapidly. These sensors have the advantages of high sensitivity, excellent selectivity, and convenience. However, the detection abundance of RNA tumor markers is low. In order to improve the detection sensitivity, researchers have developed a variety of signal amplification strategies to enhance the detection signal. In this review, after a brief introduction of the sensing principles and designs of different biosensing platforms, we will summarize the latest research progress of electrochemical, photoelectrochemical, and fluorescent biosensors based on signal amplification strategies for detecting RNA tumor markers. This review provides a high sensitivity and good selectivity sensing platform for early-stage cancer research. It provides a new idea for the development of accurate, sensitive, and convenient biological analysis in the future, which can be used for the early diagnosis and monitoring of cancer and contribute to the reduction in the mortality rate.
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Affiliation(s)
- Haiping Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
| | - Zhikun Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Lu Gan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Dianfa Fan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Xinjun Sun
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Zhangbo Qian
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Yong Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
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8
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A novel method for detection of ochratoxin A in foods—Co-MOFs based dual signal ratiometric electrochemical aptamer sensor coupled with DNA walker. Food Chem 2023; 403:134316. [DOI: 10.1016/j.foodchem.2022.134316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/23/2022]
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9
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Tetrahedral DNA framework assisted rotational paper-based analytical device for differential detection of SARS-CoV-2 and influenza A H1N1 virus. Microchem J 2023; 185:108304. [PMID: 36531593 PMCID: PMC9737512 DOI: 10.1016/j.microc.2022.108304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) and influenza A are two respiratory infectious diseases with similar clinical manifestations. Because of the complex global epidemic situation of COVID-19, the distinction and diagnosis of COVID-19 and influenza A infected persons is crucial for epidemic prevention and control. In this study, tetrahedral DNA framework (TDF) was combined with a rotational paper-based analytical device, and the color change generated by the reaction between horseradish peroxidase (HRP) and 3,3'5,5'-tetramethylbenzidine (TMB)-H2O2 was used for grayscale signal analysis by ImageJ software. The quantitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A H1N1 virus were realized simultaneously. Under the optimal conditions, the paper-based analytical device showed a good linear relationship between the two viruses in the range of 10-14-10-8g/mL, and the two viruses were not affected by cross reaction. This sensor provides a convenient and reliable method for clinical rapid differentiation and diagnosis of COVID-19 and influenza A.
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10
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Cai Q, Shi H, Sun M, Ma N, Wang R, Yang W, Qiao Z. Sensitive Detection of Salmonella Based on CRISPR-Cas12a and the Tetrahedral DNA Nanostructure-Mediated Hyperbranched Hybridization Chain Reaction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16382-16389. [PMID: 36512680 DOI: 10.1021/acs.jafc.2c05831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Salmonella severely threatens global human health and causes financial burden. The ability to sensitively detect Salmonella in food samples is highly valuable but remains a challenge. Herein, a sensitive detection method for Salmonella was developed by coupling immunomagnetic separation with the CRISPR-Cas12a system and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction (TDN-hHCR). In the detection system, the target Salmonella was immunomagnetically separated and labeled with bio-barcode DNA-modified gold nanoparticles (AuNPs), which could transfer and magnify the signal of a bacterial cell into numerous bio-barcode DNA molecules. Afterward, the bio-barcode DNA can trigger the trans-cleavage activity of CRISPR-Cas12a to inhibit the process of the TDN-hHCR to generate a fluorescence readout. Due to the high immunomagnetic separation efficiency and the effective signal amplification of CRISPR-Cas12a and the TDN-hHCR, Salmonella as low as 8 CFU/mL could be easily detected. Meanwhile, this has been applied for practical use and showed the capability to detect 17 and 25 CFU/mL in spiked milk and egg white, respectively, indicating its potential application in real samples.
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Affiliation(s)
- Qiqi Cai
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Hanxing Shi
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Mengni Sun
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Na Ma
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200438, China
| | - Wenge Yang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Zhaohui Qiao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
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11
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Shen Y, Nie C, Wei Y, Zheng Z, Xu ZL, Xiang P. FRET-based innovative assays for precise detection of the residual heavy metals in food and agriculture-related matrices. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Hybridization chain reaction and DNAzyme-based dual signal amplification strategy for sensitive fluorescent sensing of aflatoxin B1 by using the pivot of triplex DNA. Food Res Int 2022; 158:111538. [DOI: 10.1016/j.foodres.2022.111538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 11/22/2022]
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Shiu SCC, Whitehouse WL, Tanner JA. Designing aptamer-enabled DNA polyhedra using paper origami. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Recent advances in the construction of functional nucleic acids with isothermal amplification for heavy metal ions sensor. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Wang H, Xie Y, Wang Y, Lai G. Target biorecognition-triggered assembly of a G-quadruplex DNAzyme-decorated nanotree for the convenient and ultrasensitive detection of antibiotic residues. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152629. [PMID: 34963603 DOI: 10.1016/j.scitotenv.2021.152629] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/15/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
The abuse of kanamycin (Kana) in many fields has led to increasing antibiotic pollution problems and serious threats to public health. Therefore, determining how to develop methods to realize the convenient detection of antibiotics in complicated environmental matrices is highly desirable. In this study, we utilized a target biorecognition-triggered hybridization chain reaction (HCR) assembly of a G-quadruplex DNAzyme (G-DNAzyme)-decorated nanotree to develop a novel homogeneous colorimetric biosensing method for the convenient and ultrasensitive detection of Kana antibiotic residues in real samples. Through the designed aptamer-recognition reaction, an Mg2+-dependent DNAzyme (MNAzyme) strand can be liberated. Thus, its catalyzed cleavage of the hairpin substrates anchored at a DNA nanowire will cause the assembled formation of an HCR-initiator; this process can be greatly amplified by the exonuclease III-assisted target recycling and the MNAzyme-catalyzed release of another MNAzyme strand. Based on the DNA-nanowire-accelerated HCR assembly of many G-DNAzyme-decorated DNA duplexes on the two sides of the nanowire, a DNA nanotree decorated by numerous G-DNAzymes will form to realize the ultrasensitive colorimetric signal output. Under the optimal conditions, this method exhibited a wide five-order-of-magnitude linear range and a very low detection limit of 28 fg mL-1. In addition, excellent selectivity, repeatability, and reliability were also demonstrated for this homogeneous bioassay method. These unique features along with its automatic manipulation and low assay cost show promise for practical applications.
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Affiliation(s)
- Haiyan Wang
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, China
| | - Yiming Xie
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, China
| | - Yujia Wang
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, China
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, China.
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Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal. Biosens Bioelectron 2022; 197:113739. [PMID: 34781175 PMCID: PMC8553638 DOI: 10.1016/j.bios.2021.113739] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023]
Abstract
The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.
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17
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Duan N, Li C, Song M, Wang Z, Zhu C, Wu S. Signal amplification of SiO 2 nanoparticle loaded horseradish peroxidase for colorimetric detection of lead ions in water. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120342. [PMID: 34492513 DOI: 10.1016/j.saa.2021.120342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/06/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
In this work, we developed an aptamer-based optical assay for the analysis of Pb2+, a hazardous heavy metal that may be present in the food chain and harmful to human health. An aptamer targeted against Pb2+ was immobilized onto the microplate as the capture probe. SiO2 nanoparticles (NPs) were synthesized and used as carriers of the signaling horseradish peroxidase (HRP) to achieve amplification of the optical signal. Complementary DNA (cDNA) of the aptamer was also linked to the above mentioned SiO2 nanoparticle (NPs) as the signal probe. The aptamers were found to be able to capture Pb2+, and the unbound aptamers were subsequently hybridized with cDNA-HRP-SiO2 conjugates. As a result, the addition of TMB-H2O2 promoted the formation of blue products in the catalytic system. The assay adopting SiO2 NPs as an enhancer resulted in higher sensitivity with an LOD of 2.5 nM compared to normal procedures. The feasibility of the aptamer-based colorimetric assay was verified by successful detection of Pb2+ in water samples with recoveries in the range of 97.4-103.52%.
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Affiliation(s)
- Nuo Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Changxin Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingqian Song
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Changqing Zhu
- School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China.
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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Cao G, Deng Y, Chen X, Huo D, Li J, Yang M, Hou C. The fluorescent biosensor for detecting N 6 methyladenine FzD5 mRNA and MazF activity. Anal Chim Acta 2021; 1188:339185. [PMID: 34794576 DOI: 10.1016/j.aca.2021.339185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 01/11/2023]
Abstract
N6 methyladenine (m6A) modification of the FzD5 mRNA, an important post-transcriptional regulation in eukaryotes, is closely related to the occurrence and development of breast cancer. Here, we developed an ultra-sensitive biosensor based on MazF combining with cascaded strand displacement amplification (C-SDA) and CRISPR/Cas12a to detect m6A FzD5 mRNA. MazF toxin protein is a vital component of the bacterial mazEF toxin-antitoxin system that is sensitive to m6A RNA. Take advantage of it, the biosensor achieved antibody-independent and gene-specific detection for m6A RNA. Moreover, compared with traditional amplification methods, the more efficient C-SDA and the CRISPR/Cas12a system with trans-cleavage activity gave the fluorescent biosensor an excellent sensitivity with the detection limit of 0.64 fM. In addition, MazF, as a new antibacterial target, was detected by the biosensor based on C-SDA and CRISPR/Cas12a with the detection limit of 1.127 × 10-4 U mL-1. More importantly, the biosensor has good performance in complex samples. Therefore, the biosensor is a potential tool in detecting m6A FzD5 mRNA and MazF activity.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Yuanyi Deng
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Xiaolong Chen
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China
| | - Jiawei Li
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
| | - Mei Yang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Changjun Hou
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Zhou R, Zeng Z, Sun R, Liu W, Zhu Q, Zhang X, Chen C. Traditional and new applications of the HCR in biosensing and biomedicine. Analyst 2021; 146:7087-7103. [PMID: 34775502 DOI: 10.1039/d1an01371h] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hybridization chain reaction is a very popular isothermal nucleic acid amplification technology. A single-stranded DNA initiator triggers an alternate hybridization event between two hairpins forming a double helix polymer. Due to isothermal, enzyme-free and high amplification efficiency characteristics, the HCR is often used as a signal amplification technology for various biosensing and biomedicine fields. However, as an enzyme-free self-assembly reaction, it has some inevitable shortcomings of relatively slow kinetics, low cell internalization efficiency, weak biostability of DNA probes and uncontrollable reaction in these applications. More and more researchers use this reaction system to synthesize new materials. New materials can avoid these problems skillfully by virtue of their inherent biological characteristics, molecular recognition ability, sequence programmability and biocompatibility. Here, we summarized the traditional application of the HCR in biosensing and biomedicine in recent years, and also introduced its new application in the synthesis of new materials for biosensing and biomedicine. Finally, we summarized the development and challenges of the HCR in biosensing and biomedicine in recent years. We hope to give readers some enlightenment and help.
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Affiliation(s)
- Rong Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Ruowei Sun
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang 410300, Hunan, China
| | - Wenfang Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
| | - Xun Zhang
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang 410300, Hunan, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, China.
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