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Yang J, Liang Y, Li X, Zhang Y, Qian L, Ke Y, Zhang C. A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision. Angew Chem Int Ed Engl 2023; 62:e202308797. [PMID: 37691009 DOI: 10.1002/anie.202308797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.
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Affiliation(s)
- Jing Yang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yuan Liang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Xiang Li
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Long Qian
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
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Li C, Chen H, Fan T, Zhao J, Ding Z, Lin Z, Sun S, Tan C, Liu F, Jiang H, Tan Y. A visualized automatic particle counting strategy for single‐cell level telomerase activity quantification. VIEW 2023. [DOI: 10.1002/viw.20220078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Affiliation(s)
- Chen Li
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Tingting Fan
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Jingru Zhao
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Zheng Ding
- Department of Urology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology Shenzhen People's Hospital Shenzhen China
| | - Zeyu Lin
- Department of Urology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology Shenzhen People's Hospital Shenzhen China
| | - Shuqing Sun
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Feng Liu
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Hongtao Jiang
- Department of Urology Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology) Shenzhen China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology Shenzhen People's Hospital Shenzhen China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics Shenzhen International Graduate School Tsinghua University Shenzhen China
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Colorimetric detection of viral RNA fragments based on an integrated logic-operated three-dimensional DNA walker. Biosens Bioelectron 2022; 217:114714. [PMID: 36116222 DOI: 10.1016/j.bios.2022.114714] [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: 07/20/2022] [Revised: 08/28/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022]
Abstract
Timely and accurate detection of virus is crucial for preventing spread of disease and early treatment of the infected cases. Herein we design an integrated logic-operated three-dimensional DNA walker for colorimetric detection of viral RNA fragments, by taking SARS-CoV-2 as an example. The DNA walker is composed of small amounts of dually-blocked walking strands and large amounts of dual-stem-loop track strands on gold nanoparticles. The walking strand contains a swing arm domain and a DNAzyme domain blocked at both sides of catalytic core, while the track strand contains a substrate domain located at the peripheral larger loop. Only the presence of both ORF1ab and N RNA fragments can fully de-block the walking strand, which then continuously hybridizes with track strands and cleaves them by DNAzyme-catalyzed hydrolysis. As the cleavage of track strands from long-stranded, double stem-loop structure to short-stranded, linear sequence, the DNA walker shows much lowered stability due to decreased negative charge density and diminished steric repulsion, which then gets aggregated at high salt concentration, accompanied by a visible color change. The colorimetric DNA walker detects RNA fragments down to 1 nM, responds dual viral genes in a "AND" logic way, and shows high specificity to target sequence. It can further detect large nucleic acids containing ORF1ab and N sequences, and reach 200 copies/mL detection limit by coupling a simple upstream amplification of sample. The method may provide a convenient way for reliable detection of viral RNA.
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Zhang R, Zhang R, Zhao C, Xu X. A DNA tetrahedron docking assembly for imaging telomerase activity in cancerous cells. Anal Chim Acta 2022; 1193:339395. [DOI: 10.1016/j.aca.2021.339395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/01/2022]
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Yao Y, Pan H, Luo Y, Zhu D, Chao J, Su S, Wang L. A label-free electrochemical sensor for ultrasensitive microRNA-21 analysis based on the poly(l-cysteine)/MoS 2 sensing interface. Analyst 2021; 146:1663-1667. [PMID: 33480363 DOI: 10.1039/d0an02314k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The label-free detection of nucleic acids has attracted interest of scientists due to the fact that it is simple, fast and efficient. Herein, l-cysteine was electropolymerized on the molybdenum disulfide (MoS2) surface to form a stable and electroactive poly(l-cysteine)-functionalized molybdenum disulfide (Pl-Cys/MoS2) sensing interface. Taking microRNA-21 (miRNA-21) as an analytical model, a label-free electrochemical sensor was designed according to the properties of the Pl-Cys/MoS2 sensing interface. Experimental data exhibited that the designed electrochemical sensor exhibited excellent sensitivity, selectivity and stability towards miRNA-21 detection in buffer and real samples. This study offers a methodology to construct a label-free sensing interface by combining MoS2 nanosheets and electroactive molecules.
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Affiliation(s)
- Yao Yao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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Zhang R, Zhang R, Jiang W, Xu X. A multicolor DNA tetrahedron nanoprobe for analyzing human telomerase in living cells. Chem Commun (Camb) 2021; 57:2188-2191. [PMID: 33527950 DOI: 10.1039/d0cc07893j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Herein, we report the in situ analysis of human telomerase by a multicolor DNA tetrahedron nanoprobe. The elongated telomeric repeats can hybridize with settled molecular beacons in order, accompanied by sequentially lighted up fluorescence. Imaging telomerase activity, real-time monitoring telomerase action and determining product length distribution in living cells are realized. It detects multiple information of intracellular telomerase and provides deeper insights into the function of telomerase.
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Affiliation(s)
- Ruiyuan Zhang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
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Wang Y, Yang L, Wang Y, Liu W, Li B, Jin Y. Target-controlled in situ formation of G-quadruplex DNAzyme for a sensitive visual assay of telomerase activity. Analyst 2019; 144:5959-5964. [DOI: 10.1039/c9an01271k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A sensitive visual assay was developed for detecting telomerase activity based on the telomerase-controlled in situ formation of G-quadruplex-hemin DNAzyme. The telomerase activity of 5 HeLa cells per μL was visually detected in human serum.
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Affiliation(s)
- Yaocai Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Luzhu Yang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Yanjun Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Baoxin Li
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
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Xu X, Wang L, Li K, Huang Q, Jiang W. A Smart DNA Tweezer for Detection of Human Telomerase Activity. Anal Chem 2018; 90:3521-3530. [PMID: 29446916 DOI: 10.1021/acs.analchem.7b05373] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Reliable and accurate detection of telomerase activity is crucial to better understand its role in cancer cells and to further explore its function in cancer diagnosis and treatment. Here, we construct a smart DNA tweezer (DT) for detection of telomerase activity. The DT is assembled by three specially designed single-stranded oligonucleotides: a central strand dually labeled with donor/acceptor fluorophores and two arm strands containing overhangs complementary to telomerase reaction products (TRPs). It can get closed through hybridization with TRPs and get reopen through strand displacement reaction by TRPs' complementary sequences. First, under the action of telomerase, telomerase binding substrates (TS) are elongated to generate TRPs ended with telomeric repeats (TTAGGG) n. TRPs hybridize with the two arm overhangs cooperatively and strain DT to closed state, inducing an increased fluorescence resonance energy transfer (FRET) efficiency, which is utilized for telomerase activity detection. Second, upon introduction of a removal strand (RS) complementary to TRPs, the closed DT is relaxed to open state via the toehold-mediated strand displacement, inducing a decreased FRET efficiency, which is utilized for determination of TRP length distribution. The detection limit of telomerase activity is equivalent to 141 cells/μL for HeLa cells, and telomerase-active cellular extracts can be differentiated from telomerase-inactive cellular extracts. Furthermore, TRPs owning 1, 2, 3, 4, and ≥5 telomeric repeats are identified to account for 25.6%, 20.5%, 15.7%, 12.5%, and 25.7%, respectively. The proposed strategy will offer a new approach for reliable, accurate detection of telomerase activity and product length distribution for deeper studying its role and function in cancer.
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Convertible DNA ends-based silver nanoprobes for colorimetric detection human telomerase activity. Talanta 2018; 178:458-463. [DOI: 10.1016/j.talanta.2017.09.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/15/2017] [Accepted: 09/17/2017] [Indexed: 11/19/2022]
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Dual-targeting peptide probe for sequence- and structure-sensitive sensing of serum albumin. Biosens Bioelectron 2017; 94:657-662. [DOI: 10.1016/j.bios.2017.03.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 01/06/2023]
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Li K, Wang L, Xu X, Jiang W. Label-free molecular beacons-based cascade amplification DNA machine for sensitive detection of telomerase activity. Talanta 2017; 167:645-650. [DOI: 10.1016/j.talanta.2017.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/24/2017] [Accepted: 03/02/2017] [Indexed: 02/07/2023]
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