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Li H, Kou B, Yuan Y, Chai Y, Yuan R. Porous Fe 3O 4@COF-Immobilized gold nanoparticles with excellent catalytic performance for sensitive electrochemical detection of ATP. Biosens Bioelectron 2022; 197:113758. [PMID: 34798499 DOI: 10.1016/j.bios.2021.113758] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/20/2022]
Abstract
In this work, a "signal-off" electrochemical biosensor was established for sensitive detection of adenosine triphosphate (ATP) based on Fe3O4@covalent organic framework-immobilized gold nanoparticles (Fe3O4@COF-Au NPs) porous composite material as a nanocarrier. The proposed Fe3O4@COF-Au NPs could effectively confine Au NPs in the uniform channels of the Fe3O4@COF, which successfully avoided Au NPs aggregation to a certain extent and provided a comparatively independent and stable micro-environment via its hydrophobic porous nanochannels, thereby owning excellent electro-catalytic performance for the reduction of 4-nitrophenol. Moreover, the Fe3O4@COF-Au NPs nanomaterials were served as functional platform for immobilizing DNA substrate (S0), which was used to bind with the conversion product (S1) of the target ATP for subsequent branched hybridization chain reaction (b-HCR) to form dendritic DNA strands to hinder electron transfer between Fe3O4@COF-Au NPs and 4-nitrophenol, finally achieving sensitive detection of ATP with a wide linear range of 5 pM-50 μM and a low detection limit of 1.6 pM. Such strategy provides a multifunctional immobilized platform for the sensitive detection of ATP and a versatile strategy for monitoring other biomolecules.
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Affiliation(s)
- Hao Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Beibei Kou
- 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
| | - Yali Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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2
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Li CC, Hu J, Luo X, Hu J, Zhang CY. Development of a Single Quantum Dot-Mediated FRET Nanosensor for Sensitive Detection of Single-Nucleotide Polymorphism in Cancer Cells. Anal Chem 2021; 93:14568-14576. [PMID: 34672523 DOI: 10.1021/acs.analchem.1c03675] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are important hallmarks of human diseases. Herein, we develop a single quantum dot (QD)-mediated fluorescence resonance energy transfer (FRET) nanosensor with the integration of multiple primer generation rolling circle amplification (MPG-RCA) for sensitive detection of SNPs in cancer cells. This assay involves only a linear padlock probe for MPG-RCA. The presence of a mutant target facilitates the circularization of linear padlock probes to initiate RCA, producing three short single-stranded DNAs (ssDNAs) with the assistance of nicking endonuclease. The resulting ssDNAs can function as primers to induce cyclic MPG-RCA, resulting in the exponential amplification and generation of large numbers of linker probes. The linker probes can subsequently hybridize with the Cy5-labeled reporter probes and the biotinylated capture probes to obtain the sandwich hybrids. The assembly of these sandwich hybrids on the 605 nm-emission quantum dot (605QD) generates the 605QD-oligonucleotide-Cy5 nanostructures, resulting in efficient FRET from the 605QD to Cy5. This nanosensor is free from both the complicated probe design and the exogenous primers and has distinct advantages of high amplification efficiency, zero background signal, good specificity, and high sensitivity. It can detect SNPs with a large dynamic range of 8 orders of magnitude and a detection limit of 5.41 × 10-20 M. Moreover, this nanosensor can accurately distinguish as low as 0.001% mutation level from the mixtures, which cannot be achieved by previously reported methods. Furthermore, it can discriminate cancer cells from normal cells and even quantify SNP at the single-cell level.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jinping Hu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xiliang Luo
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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3
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Sun Y, Han B, Sun F. Ultra-specific genotyping of single nucleotide variants by ligase-based loop-mediated isothermal amplification coupled with a modified ligation probe. RSC Adv 2021; 11:17058-17063. [PMID: 35479710 PMCID: PMC9032167 DOI: 10.1039/d1ra00851j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/25/2021] [Indexed: 12/18/2022] Open
Abstract
Specific and accurate detection of single nucleotide variants (SNVs) plays significant roles in pathogenic gene research and clinical applications. However, the sensitive but ultra-specific detection of rare variants in biological samples still remains challenging. Herein, we report a novel, robust and practical SNV assay by integrating the outstanding features of high selectivity of an artificial mismatched probe, and the powerful loop-mediated isothermal amplification. In this strategy, we rationally introduce artificial mismatched bases into the 3′-terminal regions of the probe located in the ligation region to reduce the risk of nonspecific ligation, which can dramatically improve the specificity for the SNV assay. The proposed method can discern as little as 0.01% mutant DNA in the high background of wild-type DNA with high sensitivity (10 aM). In virtue of its outstanding performance, the artificial mismatched probe may also be employed and expanded in various DNA and RNA genetic analyses with ligase-assisted approaches, showing great potential in biomedical research, clinical diagnostics, and bioanalysis. An artificial mismatched base introduced in a ligation probe can effectively reduce nonspecific ligation and improve the specificity for SNV assay.![]()
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Affiliation(s)
- Yuanyuan Sun
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 Henan Province P. R. China .,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Bingjie Han
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 Henan Province P. R. China
| | - Fangfang Sun
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 Henan Province P. R. China
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4
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Yang D, Sun Y, Chang F, Tian H, Liu C, Li Z. Highly specific quantification of mRNA mutation in single cells based on RNase H cleavage-assisted reverse transcription (RT)-PCR. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Kim KT, Winssinger N. Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS). Chem Sci 2020; 11:4150-4157. [PMID: 34122878 PMCID: PMC8152519 DOI: 10.1039/d0sc00741b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/24/2020] [Indexed: 12/11/2022] Open
Abstract
DNA or RNA templated reactions are attractive for nucleic acid sensing and imaging. As for any hybridization-based sensing, there is a tradeoff between sensitivity (detection threshold) and resolution (single nucleotide discrimination). Longer probes afford better sensitivity but compromise single nucleotide resolution due to the small thermodynamic penalty of a single mismatch. Herein we report a design that overcomes this tradeoff. The reaction is leveraged on the hybridization of a minimal substrate (covering 4 nucleotides) which is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass the exchange of guide DNAs while achieving signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance the hybridization of short substrates by providing two π-stacking interactions. The reaction was shown to enable the detection of SNPs and SNVs down to 50 pM with a discrimination factor ranging from 24 to 309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicons obtained directly from cell culture.
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Affiliation(s)
- Ki Tae Kim
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva 30 quai Ernest Ansermet 1211 Geneva Switzerland
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6
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Zhou W, Wang L, Liu C, Teng Q, Wang Z, Dai Z. Quantification of cyclic DNA polymerization with lanthanide coordination nanomaterials for liquid biopsy. Chem Sci 2020; 11:3745-3751. [PMID: 34094063 PMCID: PMC8152624 DOI: 10.1039/c9sc06408g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/13/2020] [Indexed: 12/15/2022] Open
Abstract
Quantification of circulating tumor DNA (ctDNA) is of great importance in liquid biopsy but difficult due to its low amount in bodily fluids. To meet this high demand, a novel method for ctDNA detection is established by quantifying cyclic DNA polymerization using lanthanide coordination polymers (Ln-CPs). Relying on the coordination between the pyrophosphate ion (PPi) and trivalent cerium ion (Ce3+), organic ligand-free PPi-Ce coordination polymer networks (PPi-Ce CPNs) with enhanced fluorescence are prepared for the first time. By surveying the optical properties of PPi-Ce CPNs, it is found that PPi regulates electric-dipole transition of Ce3+ to the lowest excited state, thus facilitating the emission of fluorescence. Therefore, fluorescence enhancement of PPi-Ce CPNs originates from the ligand field effect rather than the normal antenna effect. Moreover, a new strategy to quantify DNA polymerization is developed based on PPi-Ce CPNs. By introducing multifold cyclic DNA polymerization, a small amount of ctDNA triggers the exponential generation of PPi to form plenty of PPi-Ce CPNs. Accordingly, a biosensor is constructed for sensitive ctDNA detection by measuring the intense fluorescence of PPi-Ce CPNs. The biosensor is capable of sensing ctDNA at the sub-femtomolar level, which is far better than the analytical performances of commercial dyes. Besides, the analytical method is able to detect single nucleotide polymorphism and determine ctDNA in real samples. Considering that DNA polymerization is widely used in bio-recognition, bio-assembly and biomineralization, the work provides a versatile quantitative strategy of making relevant processes precise and controllable.
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Affiliation(s)
- Wenting Zhou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University Nanjing 210023 P. R. China +86-25-85891051 +86-25-85891051
| | - Lei Wang
- Nanjing Normal University Center for Analysis and Testing Nanjing 210023 P. R. China
| | - Can Liu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University Nanjing 210023 P. R. China +86-25-85891051 +86-25-85891051
| | - Qiuyi Teng
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University Nanjing 210023 P. R. China +86-25-85891051 +86-25-85891051
| | - Zhaoyin Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University Nanjing 210023 P. R. China +86-25-85891051 +86-25-85891051
| | - Zhihui Dai
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University Nanjing 210023 P. R. China +86-25-85891051 +86-25-85891051
- Nanjing Normal University Center for Analysis and Testing Nanjing 210023 P. R. China
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Three-way junction-promoted recycling amplification for sensitive DNA detection using highly bright DNA-silver nanocluster as label-free output. Talanta 2020; 206:120216. [DOI: 10.1016/j.talanta.2019.120216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/15/2019] [Accepted: 07/31/2019] [Indexed: 12/11/2022]
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8
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Mohsen MG, Ji D, Kool ET. Polymerase synthesis of four-base DNA from two stable dimeric nucleotides. Nucleic Acids Res 2019; 47:9495-9501. [PMID: 31504784 PMCID: PMC6765132 DOI: 10.1093/nar/gkz741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 11/25/2022] Open
Abstract
We document the preparation and properties of dimerized pentaphosphate-bridged deoxynucleotides (dicaptides) that contain reactive components of two different nucleotides simultaneously. Importantly, dicaptides are found to be considerably more stable to hydrolysis than standard dNTPs. Steady-state kinetics studies show that the dimers exhibit reasonably good efficiency with the Klenow fragment of DNA polymerase I, and we identify thermostable enzymes that process them efficiently at high temperature. Experiments show that the dAp5dT dimer successfully acts as a combination of dATP and dTTP in primer extension reactions, and the dGp5dC dimer as a combination of dGTP and dCTP. The two dimers in combination promote successful 4-base primer extension. The final byproduct of the reaction, triphosphate, is shown to be less inhibitory to primer extension than pyrophosphate, the canonical byproduct. Finally, we document PCR amplification of DNA with two dimeric nucleotides, and show that the dimers can promote amplification under extended conditions when PCR with normal dNTPs fails. These dimeric nucleotides represent a novel and simple approach for increasing stability of nucleotides and avoiding inhibition from pyrophosphate.
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Affiliation(s)
- Michael G Mohsen
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Debin Ji
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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9
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Zhao Y, Fang X, Chen F, Bai M, Fan C, Zhao Y. Locus-patterned sequence oriented enrichment for multi-dimensional gene analysis. Chem Sci 2019; 10:8421-8427. [PMID: 31803421 PMCID: PMC6844269 DOI: 10.1039/c9sc02496d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/22/2019] [Indexed: 11/21/2022] Open
Abstract
Multi-dimensional gene analysis provides in-depth insights into gene sequence, locus variations and molecular abundance, whereas it is vulnerable to the perturbation of complex reaction networks and always compromises on the discrimination of analogous sequences. Here, we present a sequence oriented enrichment method patterned by the prescribed locus without crosstalk between concurrent reactions. Energetically favourable structures of nucleic acid probes are theoretically derived and oriented to a specific gene locus. We designed a pair of universal probes for multiple conserved loci to avoid side reactions from undesired interactions among increased probe sets. Furthermore, competitive probes were customized to sink analogues for differentiating the reaction equilibrium and kinetics of sequence enrichment from the target, so variant loci can be synchronously identified with nucleotide-level resolution. Thus, the gene locus guides sequence enrichment and combinatorial signals to create unique codes, which provides access to multidimensional and precise information for gene decoding.
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Affiliation(s)
- Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Xiaoxing Fang
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering , Institute of Molecular Medicine , Renji Hospital , School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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