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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] [MESH Headings] [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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2
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Jiang H, Peng Z, Lv X, Liu Y, Li X, Deng Y. Hybrid chain reaction nanoscaffold-based functional nucleic acid nanomaterial cascaded with rolling circle amplification for signal enhanced miRNA let-7a detection. Mikrochim Acta 2024; 191:533. [PMID: 39134753 DOI: 10.1007/s00604-024-06617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024]
Abstract
A novel functional nucleic acid (FNA) nanomaterial based on hybrid chain reaction (HCR) nanoscaffolds is proposed to solve the problem of time superposition and repeated primer design in sensitive miRND detection using cascade amplification technique. Rolling circle amplification (RCA) was cascaded with the prepared FNA nanomaterials for miRNA let-7a (as a model target) sensitive detection by lateral flow assay (LFA). Under the optimal conditions, the proposed RCA-FNA-LFA assay demonstrated the specificity and accuracy for miRNA let-7a detection with a detection limit of 1.07 pM, which increased sensitivity by nearly 20 times compared with that of RCA -LFA assay. It is worth noting that the non-target-dependent self-assembly process of HCR nanoscaffolds does not take up the whole detection time, thus, less time is taken than that of the conventional cascaded method. Moreover, the proposed assay does not need to consider the system compatibility between two kinds of isothermal amplification techniques. As for detection of different miRNAs, only the homologous arm of the padlock probe of RCA needs to be changed, while the FNA nanomaterial does not need any change, which greatly simplifies the primer design of the cascaded amplification techniques. With further development, the proposed RCA-FNA-LFA assay might achieve more sensitive and faster results to better satisfy the requirements of clinical diagnosis combing with more sensitive labels or small strip reader.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhao Peng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Ying Liu
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
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3
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Dou S, Liu M, Wang H, Zhou S, Marrazza G, Guo Y, Sun X, Darwish IA. Synthesis of dual models multivalent activatable aptamers based on HCR and RCA for ultrasensitive detection of Salmonella typhimurium. Talanta 2024; 275:126101. [PMID: 38631268 DOI: 10.1016/j.talanta.2024.126101] [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: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
Aptamers have superior structural properties and have been widely used in bacterial detection methods. However, the problem of low affinity still exists in complex sample detection. In contrast, hybridization chain reaction (HCR)-based model I and rolling circle amplification (RCA)-based model II multivalent activatable aptamers (multi-Apts) can fulfill the need for low-cost, rapid, highly sensitive and high affinity detection of S. typhimurium. In our research, two models of multi-Apts were designed. First, a monovalent activatable aptamer (mono-Apt) was constructed by fluorescence resonance energy transfer (FRET) with an S. typhimurium aptamer and its complementary chain of BHQ1. Next, the DNA scaffold was obtained by HCR and RCA, and the multi-Apts were obtained by self-assembly of the mono-Apt with a DNA scaffold. In model I, when target was presented, the complementary chain BHQ1 was released due to the binding of multi-Apts to the target and was subsequently adsorbed by UIO66. Finally, a FRET-based fluorescence detection signal was obtained. In mode II, the multi-Apts bound to the target, and the complementary chain BHQ1 was released to become the trigger chain for the next round of amplification of HCR with a fluorescence detection signal. HCR and RCA based multi-Apts were able to detect S. typhimurium as low as 2 CFU mL-1 and 1 CFU mL-1 respectively. Multi-Apts amplification strategy provides a new method for early diagnosis of pathogenic microorganisms in foods.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Shuxian Zhou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Giovanna Marrazza
- "Ugo Schiff" Chemistry Department, University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
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Yan T, Hou Y, Zuo Q, Jiang D, Zhao H, Xia T, Zhu X, Han X, An R, Liang X. Ultralow background one-pot detection of Lead(II) using a non-enzymatic double-cycle system mediated by a hairpin-involved DNAzyme. Biosens Bioelectron 2023; 237:115534. [PMID: 37527624 DOI: 10.1016/j.bios.2023.115534] [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: 05/10/2023] [Revised: 07/01/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
A double-cycle system has been developed for specifically detecting trace amounts of Pb2+ by significantly decreasing the background signal. The detection involves two types of RNA cleavage reactions: one using a Pb2+-specific GR5 DNAzyme (PbDz) and the other utilizing a newly constructed 10-23 DNAzyme with two hairpins embedded in its catalytic center (hpDz). The ring-structured hpDz (c-hpDz) exhibits significantly lower activity compared to the circular 10-23 DNAzyme without hairpin structures, which plays a crucial role in reducing the background signal. When Pb2+ is present, PbDz cleaves c-hpDz to its active form, which then disconnects the molecular beacon to emit the fluorescent signal. The method allows for rapid and sensitive Pb2+ detection within 40 min for 10 fM of Pb2+ and even as short as 10 min for 100 nM of Pb2+. Additionally, visual detection is possible through the non-crosslinking assembly of Au nanoparticles. The entire process can be performed in one pot and even one step, making it highly versatile and suitable for a wide range of applications, including food safety testing and environmental monitoring.
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Affiliation(s)
- Ting Yan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Yuying Hou
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Qianqian Zuo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Difei Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Huijie Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Tongyue Xia
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Xiaoqian Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Xutiange Han
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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5
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Li Y, Ma X, Liu K, Liu Z, Zou R, Wang J, Yang C, Zheng H, Sun C. A ratiometric fluorescence platform for lead ion detection via RNA cleavage-inhibited self-assembly of three-arm branched junction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 298:122787. [PMID: 37150075 DOI: 10.1016/j.saa.2023.122787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
Heavy metal pollution can pose a threat to food safety and human health, and accurate quantification of heavy metal ions is a vital requirement. Emerging DNA nanostructures-based biosensors offer attractive tools toward ultra-sensitive or rapid analysis of heavy metal ions. However, the problems including complex design, severe reaction conditions and undesirable reliability are inevitable obstacle in advancing their extension and application. Herein, a ratiometric fluorescent platform was established for monitoring lead ion (Pb2+) in food based on dual Förster resonance energy transfer (FRET) and RNA cleavage-inhibited self-assembly of three-arm branched junction (TBJ). GR-5 DNAzyme was employed for Pb2+ recognition, and enzyme-free amplification technique catalytic hairpin assembly (CHA) served to form FRET probes-carried TBJ. The substrate strand (S) of DNAzyme triggered the generation of CHA-TBJ, and Pb2+-responsive cleavage of S hindered the assembly of CHA-TBJ, causing opposite changes in the FRET states of FAM/BHQ1 and ROX/BHQ2 pairs. The fluorescence responses were recorded through synchronous fluorescence spectrometry to indicate Pb2+ concentration, allowing sensitive and reliable identification of Pb2+ in the linear range of 0.05-5 ng mL-1 with the detection limit of 0.03 ng mL-1. The Pb2+ detection can be achieved under conventional reaction conditions, simple mixing procedures and one-step measurement operation. The approach can afford excellent specificity for Pb2+ against competing metal ions, and can be applied to analyze Pb2+ in tea samples with satisfactory results. This facile fluorescence platform shows a capable method for Pb2+ detection, and provides new avenue in the development of ratiometric approaches and DNAzyme strategies for monitoring heavy metal pollution, facilitating the transformation of DNAzyme-based biosensors for food safety control.
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Affiliation(s)
- Ying Li
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Xinyue Ma
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Kai Liu
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Zheng Liu
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Ruiqi Zou
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Junyang Wang
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Chuanyu Yang
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China
| | - Hongru Zheng
- Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, Jilin, China
| | - Chunyan Sun
- Department of Food Quality and Safety, Jilin University, Changchun 130062, China.
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6
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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: 20] [Impact Index Per Article: 6.7] [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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7
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Li Y, Su R, Li H, Guo J, Hildebrandt N, Sun C. Fluorescent Aptasensors: Design Strategies and Applications in Analyzing Chemical Contamination of Food. Anal Chem 2021; 94:193-224. [PMID: 34788014 DOI: 10.1021/acs.analchem.1c04294] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Ruifang Su
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique: Réactivité et Analyse), UMR 6014, CNRS, Université de Rouen Normandie, INSA, 76821 Mont-Saint-Aignan Cedex, France
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Jiajia Guo
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055 Shenzhen, China
| | - Niko Hildebrandt
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique: Réactivité et Analyse), UMR 6014, CNRS, Université de Rouen Normandie, INSA, 76821 Mont-Saint-Aignan Cedex, France.,Université Paris-Saclay, 91190 Saint-Aubin, France.,Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
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Zhang Y, Zhao J, Yang G, He Y, Chen S, Yuan R. Ultrasensitive Detection of Amyloid β Oligomers Based on the "DD-A" FRET Binary Probes and Quadrivalent Cruciform DNA Nanostructure-Mediated Cascaded Amplifier. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32013-32021. [PMID: 34212714 DOI: 10.1021/acsami.1c07598] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The reported donor donor-acceptor ("DD-A") fluorescence resonance energy transfer (FRET) was typically achieved through random collisions and interactions of DNA molecules in the bulk solution, which has inevitable defects, including weak biological stability, slow reaction kinetics, and low hybridization efficiency. In order to overcome these deficiencies, this work developed a quadrivalent cruciform DNA nanostructure (qCDN)-mediated cascaded catalyzed hairpin assembly (CHA) amplifier for the fluorescence detection of amyloid β oligomer species (AβOs). First, four H1 and four H2 hairpins were assembled on one qCDN to obtain qCDNH1 and qCDNH2, respectively. In the presence of AβOs, strand C was released from the P1-C hybrid hairpin and then alternately opened qCDNH1 and qCDNH2 to trigger the qCDN-mediated CHA. As a result, double donors in H1 and one acceptor in H2 were mutually closed, and the porous DNA nanonet with a high loading of "DD-A" FRET binary probes was formed. The FRET efficiency was approximately 78%, and the initial reaction rate was 25-fold faster than the conventional CHA. The detection limit of AβOs was as low as 0.69 pM. The combination of the "DD-A" FRET binary probes and qCDN-mediated cascaded amplifier exhibited great promise for detecting biomarkers with trace levels.
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Affiliation(s)
- Yuanyuan 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
| | - Jinwen Zhao
- 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
| | - Guomin 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 He
- 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
| | - Shihong Chen
- 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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9
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Liu L, Han L, Wu Q, Sun Y, Li K, Liu Y, Liu H, Luo E. Multifunctional DNA dendrimer nanostructures for biomedical applications. J Mater Chem B 2021; 9:4991-5007. [PMID: 34008692 DOI: 10.1039/d1tb00689d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA nanomaterials have attracted ever-increasing attention over the past decades due to their incomparable programmability and multifunctionality. In particular, DNA dendrimer nanostructures, as a major research focus, have been applied in the fields of biosensing, therapeutics, and protein engineering, benefiting from their highly branched configuration. With the aid of specific recognition probes and inherent signal amplification, DNA dendrimers can achieve ultrasensitive detection of nucleic acids, proteins, cells, and other substances, such as lipopolysaccharides (LPS), adenosine triphosphate (ATP), and exosomes. By virtue of their void-containing structures and biocompatibility, DNA dendrimers can deliver drugs or functional nucleic acids into target cells in chemotherapy, immunotherapy, and gene therapy. Furthermore, DNA dendrimers are being applied in protein engineering for efficient directed evolution of proteins. This review summarizes the main research progress of DNA dendrimers, concerning their assembly methods and biomedical applications as well as the emerging challenges and perspectives for future research.
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Affiliation(s)
- Linan Liu
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
| | - Lichi Han
- Department of Stomatology, Medical College, Dalian University, Dalian, Liaoning 116622, P. R. China
| | - Qionghui Wu
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
| | - Yue Sun
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
| | - Kehan Li
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
| | - Yao Liu
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
| | - Hanghang Liu
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
| | - En Luo
- State Key Laboratory of Oral Disease & National Clinical Research Center for Oral Diseases & Department of Oral Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China.
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10
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Xu L, Duan J, Chen J, Ding S, Cheng W. Recent advances in rolling circle amplification-based biosensing strategies-A review. Anal Chim Acta 2020; 1148:238187. [PMID: 33516384 DOI: 10.1016/j.aca.2020.12.062] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 01/12/2023]
Abstract
Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.
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Affiliation(s)
- Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jiaxin Duan
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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Yang Y, Li W, Liu J. Review of recent progress on DNA-based biosensors for Pb 2+ detection. Anal Chim Acta 2020; 1147:124-143. [PMID: 33485571 DOI: 10.1016/j.aca.2020.12.056] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/12/2020] [Accepted: 12/25/2020] [Indexed: 02/08/2023]
Abstract
Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb2+ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb2+ has become a rapidly growing topic in the analytical community. Pb2+ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb2+ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb2+ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb2+ sensing. In this article, these Pb2+ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.
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Affiliation(s)
- Yongjie Yang
- Department of Food and Biological Sciences, College of Agriculture, Yanbian University, Yanji, 133002, China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Weixuan Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada; Water Institute, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
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