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Liu H, Yang X, Huang B, Liu H. A universal approach for synthesis of copper nanoclusters templated by G-rich oligonucleotide sequences and their applications in sensing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122740. [PMID: 37080047 DOI: 10.1016/j.saa.2023.122740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Herein, five common G4 sequences have been selected, including three different length of telomere DNA, hemin aptamer, and thrombin aptamer, to synthesize Cu nanoclusters (Cu NCs) in-situ. All G4s are proper templates for Cu NCs with low temperature treatment. The particles (G4-Cu NCs) smaller than 3 nm in diameter were obtained and showed light green fluorescence. This is the first report of metal clusters templated by G4s in-situ. As proof of the concept, hemin and alkaline phosphatase (ALP) were used as the targets to test whether the system can monitor the interaction between G4s and its substrate. The results suggest that G4-Cu NCs can indicate the behavior of G4 and its interaction with hemin, and sensing ALP is achieved with the aid of ATP. The linear ranges of hemin and ALP are 300-4000 nM and 10-500 U/L, respectively, and the corresponding limits of detection as low as 97 nM for hemin and 2.8 U/L for ALP. Moreover, this present system has been successfully applied for the detection of ALP in human serum samples with satisfactory recoveries. This synthesis approach is universal, and it can be easily extended to evaluating the formation of G4, or monitoring the interaction between G4 and its substrate, or selective targeting individual G4, or sensitive detection of other important biomarkers by changing template G4 sequence.
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Affiliation(s)
- Hong Liu
- Department of Head and Neck Cancer Center, Chongqing University Cancer Hospital &Chongqing Cancer Institute, Chongqing 400000, China
| | - Xuliang Yang
- Department of Thoracic Surgery, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400000, China
| | - Bo Huang
- Department of Thoracic Surgery, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400000, China
| | - Hongxiang Liu
- Department of Thoracic Surgery, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing 400000, China.
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Yang X, Liu X, Kang Q, Qi Y, Du Y, Xiang H. A novel DNA detection using spherical identification probe and strand displacement reaction-initiated silver nanocluster switch. ANAL SCI 2023; 39:275-284. [PMID: 36607557 PMCID: PMC9816546 DOI: 10.1007/s44211-022-00243-y] [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: 09/26/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
Abstract
Herein, we developed a novel fluorescent assay using spherical identification probes and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch. In this strategy, the target was captured by the spherical probes to induce the activity of exonuclease III (Exo III), catalyzing the cyclic cleavage of substrates to produce a mass of trigger strands. After magnetic bead separation, the intermediates in the supernatant activated downstream toehold-mediated strand displacement reaction to change the structure of silver nanocluster templates, leading to fluorescence intensity reduction. Furthermore, it is demonstrated that the application of spherical identification probes could reduce the signal leakage and the limit of detection. In addition, AgNCs with perfect optical property were ingeniously combined to realize signal output, which reduced the cost and time of synthesis. Under the optimal conditions, the sensing method displayed a good linear range from 250 pM to 25 nM with a detectable minimum concentration of 250 pM. And the practical application potential in complex biological matrices was also evaluated. Considering these advantages, this constructed strategy opens a new path for nucleic acid detection with better performance. A simple, label- and hairpin-free fluorescent system based on spherical identification probe and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch was successfully constructed to detect target DNA.
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Affiliation(s)
- Xiaoyan Yang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, Guang’an People’ Hospital, Guang’an, People’s Republic of China
| | - Qi Kang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Yinxiao Qi
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Yumin Du
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 People’s Republic of China
| | - Hua Xiang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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Chen J, Liu J, Wu D, Pan R, Chen J, Wu Y, Huang M, Li G. CRISPR/Cas Precisely Regulated DNA-Templated Silver Nanocluster Fluorescence Sensor for Meat Adulteration Detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14296-14303. [PMID: 36288511 DOI: 10.1021/acs.jafc.2c04500] [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: 06/16/2023]
Abstract
Meat adulteration can cause consumer fraud, food allergies, and religious issues. Rapid and sensitive detection methods are urgently demanded to supervise meat authenticity. Herein, a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas precisely regulated DNA-templated silver nanocluster (DNA-AgNC) sensor was ingeniously designed to detect meat adulteration. Specific sequence recognition of CRISPR/Cas12a allowed accurate identification of target DNA. The emerging label-free fluorescent probes, DNA-AgNCs, a class of promising fluorophores in biochemical analysis with attractive photostability and remarkably enhanced fluorescence properties, were first introduced as the substrates of CRISPR/Cas12a system, allowing a sensitive output of amplified signals through the precise regulation of the unique target DNA-activated trans-cleavage activity of Cas12a. Based on this specific recognition, efficient signal transduction of CRISPR/Cas12a, and the outstanding fluorescence properties of DNA-AgNCs, the proposed strategy achieved a satisfactory linear range from 10 pM to 1 μM with a limit of detection (LOD) as low as 1.9 pM, which can achieve sensitive detection of meat adulteration.
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Affiliation(s)
- Jiahui Chen
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jianghua Liu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, U.K
| | - Ruiyuan Pan
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Jian Chen
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Mingquan Huang
- Beijing Laboratory of Food Quality and Safety, Beijing Technology and Business University, Beijing 100048, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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Dai R, Zhang Y, Huang K, Peng X. Recent advances in the visual detection of ions and molecules based on gold and silver nanoclusters. ANALYTICAL METHODS 2022; 14:2820-2832. [PMID: 35843220 DOI: 10.1039/d2ay00618a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gold and silver nanoclusters (Au/AgNCs) exhibit excellent application potential in optical biosensors because of their low toxicity, excellent biocompatibility, and unique optical properties. Au/AgNCs-based visual analysis methods have emerged as powerful tools for detecting various targets with convenient readout. In this review, the applications of Au/AgNCs in the visual detection and bioimaging of metal ions, inorganic anions, small molecules, and biomacromolecules in various devices are summarized. Furthermore, this review also discusses the future perspectives of the field.
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Affiliation(s)
- Rui Dai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Yixin Zhang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Ke Huang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan, 610068, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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Guo Y, Wang M, Zhang W, Yu H, Cheng Y, Xie Y, Ding H, Yao W, Qian H. Detection of Norovirus RNA based on catalytic hairpin assembly and magnetic separation of DNA AgNCs. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Orientational screening of ssDNA-templated silver nanoclusters and application for bleomycin assay. Colloid Polym Sci 2021. [DOI: 10.1007/s00396-021-04890-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing. Talanta 2021; 226:122146. [PMID: 33676697 DOI: 10.1016/j.talanta.2021.122146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.
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Feng Z, Zhang W, Li L, Tu B, Ye W, Tang X, Wang H, Xiao X, Wu T. A cost-effective detection of low-abundance mutation with DNA three-way junction structure and lambda exonuclease. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Guo Y, Wang M, Shen F, Hu Z, Ding H, Yao W, Qian H. Sensitive detection of RNA based on concatenated self-fuelled strand displacement amplification and hairpin-AgNCs. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:447-452. [PMID: 33355546 DOI: 10.1039/d0ay01762k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herein, a self-fuelled amplification strategy (SFAS) is proposed, in which two strand displacement amplification (SDA) processes were concatenated for the proliferation of ssDNA. The ssDNA then initiated a polymerase action and caused the destruction of hairpin-templated silver nanoclusters (AgNCs), resulting in decreased fluorescence for sensing miRNA-21. This SFAS-based sensor is less complicated in design and facile in operation, because of the easy concatenation of SDA and mutual enzymes used in the signal output process. The sensitivity of this SFAS-based miRNA sensor was 1.78 × 10-11 M with a linear relationship in the range 0.02-1.0 × 10-9 M, and the recoveries of this method ranged from 82.07% to 106.58% with an average RSD of 10.96%.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China.
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Wang X, Tao Z. Expanding the analytical applications of nucleic acid hybridization using junction probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4931-4938. [PMID: 33043948 DOI: 10.1039/d0ay01605e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
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Liu G, Ma X, Tang Y, Miao P. Ratiometric fluorescence method for ctDNA analysis based on the construction of a DNA four-way junction. Analyst 2020; 145:1174-1178. [PMID: 32016264 DOI: 10.1039/d0an00044b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present a novel ratiometric fluorescent biosensor for ctDNA analysis based on the construction of a DNA four-way junction (FWJ). Three fuel strands for the FWJ are firstly designed and prepared. Another essential strand for the formation of the structure is the DNA product generated from target ctDNA initiated strand displacement amplification. With the transformation of the DNA structure, the FRET states of two fluorophores change and the ratiometric fluorescence response can be recorded to indicate the level of the initial ctDNA. The proposed method also has excellent capability to discriminate mismatches and shows potential practical utility for clinical samples.
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Affiliation(s)
- Guangxing Liu
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, China.
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12
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Guo Y, Shen F, Cheng Y, Yu H, Xie Y, Yao W, Pei R, Qian H, Li HW. DNA-Hairpin-Templated Silver Nanoclusters: A Study on Stem Sequence. J Phys Chem B 2020; 124:1592-1601. [PMID: 32045529 DOI: 10.1021/acs.jpcb.9b09741] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA hairpins are widely used to synthesize silver nanoclusters (AgNCs) with excellent optical properties due to their specific secondary structure. Hairpin-AgNCs have been popularly employed for sensoring applications, while no systematic study has been done about the effect of stem sequence on the fluorescence property of hairpin-AgNCs. In this presented work, the synthesizing conditions of hairpin-AgNCs were fully examined first. Then, the effect of percentage content and distribution of GC base pairs as well as stem length on the fluorescence property of hairpin-AgNCs were studied. Intriguing phenomena were observed and basic conclusions were drawn, which would be helpful to understand the hairpin-AgNCs comprehensively and instructional for the applications using hairpin-AgNC probes.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Fumiao Shen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Ruoshui Road, Suzhou 215123, China
| | - He Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hung-Wing Li
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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