1
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Chakraborty S, Pramanik S, Shekhar S, Mukherjee S. Plasmon-emitter coupling in cytosine-rich hairpin DNA-templated silver nanoclusters: Thermal reversibility, white light emission, and dynamics inside live cells. J Chem Phys 2024; 160:154303. [PMID: 38624117 DOI: 10.1063/5.0200544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
Bio-templated luminescent noble metal nanoclusters (NCs) have attracted great attention for their intriguing physicochemical properties. Continuous efforts are being made to prepare NCs with high fluorescence quantum yield (QY), good biocompatibility, and tunable emission properties for their widespread practical applications as new-generation environment-friendly photoluminescent materials in materials chemistry and biological systems. Herein, we explored the unique photophysical properties of silver nanoclusters (AgNCs) templated by cytosine-rich customized hairpin DNA. Our results indicate that a 36-nucleotide containing hairpin DNA with 20 cytosine (C20) in the loop can encapsulate photostable red-emitting AgNCs with an absolute QY of ∼24%. The luminescent properties in these DNA-templated AgNCs were found to be linked to the coupling between the surface plasmon and the emitter. These AgNCs exhibited excellent thermal sensitivity and were employed to produce high-quality white light emission with an impressive color rendering index of 90 in the presence of dansyl chloride. In addition, the as-prepared luminescent AgNCs possessing excellent biocompatibility can effectively mark the nuclear region of HeLa cells and can be employed as a luminescent probe to monitor the cellular dynamics at a single molecular resolution.
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Affiliation(s)
- Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Shashi Shekhar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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2
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Tang Q, Li Q, Shi L, Liu W, Li B, Jin Y. Multifunctional DNA nanoprobe for tumor-targeted synergistic therapy by integrating chemodynamic therapy with gene silencing. NANOSCALE HORIZONS 2023; 8:1106-1112. [PMID: 37317707 DOI: 10.1039/d2nh00575a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Due to the high complexity, diversity and heterogeneity of tumor occurrence and development, multi-mode synergistic therapy is more effective than single treatment modes to improve the antitumor efficacy. Also, multifunctional probes are crucial to realize synergistic therapy. Herein, a multifunctional DNA tetrahedron nanoprobe was ingeniously designed to simultaneously achieve chemodynamic therapy (CDT) and gene silencing for synergistic antitumor. The multifunctional DNA tetrahedron nanoprobe, DNA tetrahedron-silver nanocluster-antagomir-21 (D-sgc8-DTNS-AgNCs-Anta-21), integrated a CDT reagent (DNA-AgNCs) and miRNA-21 inhibitor (Anta-21) with a specific recognition probe (aptamer). After targeted entry in cancer cells, D-sgc8-DTNS-AgNCs-Anta-21 silenced endogenous miRNA-21 by Anta-21 and produced highly toxic ˙OH by reacting with H2O2, which induced apoptosis in the tumor cells. The targeted recognition of aptamers led to the concentration-dependent death of HeLa cells. On the contrary, the cell survival rate of normal cells was basically unaffected with an increase in the concentration of D-sgc8-DTNS-AgNCs-Anta-21. Therefore, the diverse functions, biocompatibility and programmability of DNA provide a useful and easy way to assemble multifunctional probes for synergistic therapy.
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Affiliation(s)
- Qiaorong Tang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Qianqian Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Wei Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
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3
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García JF, Reguera D, Valls A, Aviñó A, Dominguez A, Eritja R, Gargallo R. Detection of pyrimidine-rich DNA sequences based on the formation of parallel and antiparallel triplex DNA and fluorescent silver nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122752. [PMID: 37084680 DOI: 10.1016/j.saa.2023.122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
In this work, the use of DNA-stabilized fluorescent silver nanoclusters for the detection of target pyrimidine-rich DNA sequences by formation of parallel and antiparallel triplex structures is studied by molecular fluorescence spectroscopy. In the case of parallel triplexes, the probe DNA fragments are Watson-Crick stabilized hairpins, and whereas in the case of antiparallel triplexes, the probe fragments are reverse-Hoogsteen clamps. In all cases, the formation of the triplex structures has been assessed by means of polyacrylamide gel electrophoresis, circular dichroism, and molecular fluorescence spectroscopies, as well as multivariate data analysis methods. The results have shown that it is possible the detection of pyrimidine-rich sequences with an acceptable selectivity by using the approach based on the formation of antiparallel triplex structures.
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Affiliation(s)
- Juan Fernando García
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - David Reguera
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Andrea Valls
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Arnau Dominguez
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain.
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4
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Molaabasi F, Kefayat A, Ghasemzadeh A, Amandadi M, Shamsipur M, Alipour M, Moosavifard SE, Besharati M, Hosseinkhani S, Sarrami-Forooshani R. Role of the Probe Sequence/Structure in Developing an Ultra-Efficient Label-Free COVID-19 Detection Method Based on Competitive Dual-Emission Ratiometric DNA-Templated Silver Nanoclusters as Single Fluorescent Probes. Anal Chem 2022; 94:17757-17769. [PMID: 36512507 PMCID: PMC9762418 DOI: 10.1021/acs.analchem.2c02189] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
We report the development of a label-, antibody-, enzyme-, and amplification-free ratiometric fluorescent biosensor for low-cost and rapid (less than 12 min) diagnosis of COVID-19 from isolated RNA samples. The biosensor is designed on the basis of cytosine-modified antisense oligonucleotides specific for either N gene or RdRP gene that can form silver nanoclusters (AgNCs) with both green and red emission on an oligonucleotide via a one-step synthesis process. The presence of the target RNA sequence of SARS-CoV-2 causes a dual-emission ratiometric signal transduction, resulting in a limit of detection of 0.30 to 10.0 nM and appropriate linear ranges with no need for any further amplification, fluorophore, or design with a special DNA fragment. With this strategy, five different ratiometric fluorescent probes are designed, and how the T/C ratio, the length of the stem region, and the number of cytosines in the loop structure and at the 3' end of the cluster-stabilizing template can affect the biosensor sensitivity is investigated. Furthermore, the effect of graphene oxide (GO) on the ratiometric behavior of nanoclusters is demonstrated and the concentration-/time-dependent new competitive mechanism between aggregation-caused quenching (ACQ) and aggregation-induced emission enhancement (AIE) for the developed ssDNA-AgNCs/GO nanohybrids is proposed. Finally, the performance of the designed ratiometric biosensor has been validated using the RNA extract obtained from more than 150 clinical samples, and the results have been confirmed by the FDA-approved reverse transcription-polymerase chain reaction (RT-PCR) diagnostic method. The diagnostic sensitivity and specificity of the best probe is more than >90%, with an area under the receiver operating characteristic (ROC) curve of 0.978.
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Affiliation(s)
- Fatemeh Molaabasi
- Biomaterials
and Tissue Engineering Research Group, Department of Interdisciplinary
Technologies, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran 1517964311, Iran
| | - Amirhosein Kefayat
- Department
of Oncology, Cancer Prevention Research
Center, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Abbas Ghasemzadeh
- ATMP
Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran1517964311, Iran
| | - Mojdeh Amandadi
- Department
of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Mojtaba Shamsipur
- Department
of Chemistry, Razi University, Kermanshah 67144-14971, Iran
| | - Mozhgan Alipour
- Department
of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Seyyed Ebrahim Moosavifard
- Department
of Advanced Medical Sciences & Technologies, School of Medicine, Jahrom University of Medical Sciences, Jahrom 74148-46199, Iran
| | - Maryam Besharati
- Department
of Advanced Technologies, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd 94149-74877, Iran
| | - Saman Hosseinkhani
- Department
of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Ramin Sarrami-Forooshani
- ATMP
Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran1517964311, Iran
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5
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Cheng Y, Li G, Huang X, Qian Z, Peng C. Label-Free Fluorescent Turn-On Glyphosate Sensing Based on DNA-Templated Silver Nanoclusters. BIOSENSORS 2022; 12:bios12100832. [PMID: 36290969 PMCID: PMC9599485 DOI: 10.3390/bios12100832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 05/31/2023]
Abstract
In this work, a label-free fluorescent detection method for glyphosate, based on DNA-templated silver nanoclusters (DNA-Ag NCs) and a Cu2+-ion-modulated strategy, was developed. In the presence of Cu2+, the fluorescence of the DNA-Ag NCs was quenched. Glyphosate can restore the fluorescence of DNA-Ag NCs. By analyzing the storage stability of the obtained DNA-Ag NCs using different DNA templates, specific DNA-Ag NCs were selected for the construction of the glyphosate sensor. The ultrasensitive detection of glyphosate was achieved by optimizing the buffer pH and Cu2+ concentration. The sensing of glyphosate demonstrated a linear response in the range of 1.0-50 ng/mL. The limit of detection (LOD) was 0.2 ng/mL. The proposed method was successfully applied in the detection of glyphosate in a real sample, indicating its high application potential for glyphosate detection.
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Affiliation(s)
- Yuliang Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Guowen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Xiufang Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Zhijuan Qian
- Nanjing Customs District Light Industry 375 Productsand Children’s Products Inspection Center, Yangzhou 225009, China
| | - Chifang Peng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
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6
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Nagda R, Park S, Jung IL, Nam K, Yadavalli HC, Kim YM, Yang K, Kang J, Thulstrup PW, Bjerrum MJ, Cho M, Kim TH, Roh YH, Shah P, Yang SW. Silver Nanoclusters Serve as Fluorescent Rivets Linking Hoogsteen Triplex DNA and Hairpin-Loop DNA Structures. ACS NANO 2022; 16:13211-13222. [PMID: 35952305 DOI: 10.1021/acsnano.2c06631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Greater understanding of the mutual influence between DNA and the associated nanomaterial on the properties of each other can provide alternative strategies for designing and developing DNA nanomachines. DNA secondary structures are essential for encapsulating highly emissive silver nanoclusters (DNA/AgNCs). Likewise, AgNCs stabilize secondary DNA structures, such as hairpin DNA, duplex DNA, and parallel-motif DNA triplex. In this study, we found that the fluorescence of AgNCs encapsulated within a Hoogsteen triplex DNA structure can be turned on and off in response to pH changes. We also show that AgNCs can act as nanoscale rivets, linking two functionally distinctive DNA nanostructures. For instance, we found that a Hoogsteen triplex DNA structure with a seven-cytosine loop encapsulates red fluorescent AgNCs. The red fluorescence faded under alkaline conditions, whereas the fluorescence was restored in a near-neutral environment. Hairpin DNA and random DNA structures did not exhibit this pH-dependent AgNCs fluorescence. A fluorescence lifetime measurement and a small-angle X-ray scattering analysis showed that the triplex DNA-encapsulated AgNCs were photophysically convertible between bright and dark states. An in-gel electrophoresis analysis indicated that bright and dark convertibility depended on the AgNCs-riveted dimerization of the triplex DNAs. Moreover, we found that AgNCs rivet the triplex DNA and hairpin DNA to form a heterodimer, emitting orange fluorescence. Our findings suggest that AgNCs between two cytosine-rich loops can be used as nanorivets in designing noncanonical DNA origami beyond Watson-Crick base pairing.
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Affiliation(s)
- Riddhi Nagda
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sooyeon Park
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Il Lae Jung
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon 34057, Korea
| | - Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hari Chandana Yadavalli
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Kyungjik Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jooyoun Kang
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
| | | | | | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Tae-Hwan Kim
- Department of Quantum System Engineering, Jeonbuk National University, Jeonju 54896, Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Pratik Shah
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- Department of Science and Environment, Roskilde University, Roskilde 4000, Denmark
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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7
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Zhan S, Jiang J, Zeng Z, Wang Y, Cui H. DNA-templated coinage metal nanostructures and their applications in bioanalysis and biomedicine. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Yin L, Zhang H, Wang Y, He L, Lu L. Exploring the fluorescence enhancement of the split G-quadruplex towards DNA-templated AgNCs and their application in omethoate detection. J Mater Chem B 2022; 10:8856-8861. [DOI: 10.1039/d2tb01755e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Based on the enhancement of split G-quadruplex on the fluorescence of DNA-templated AgNCs, a facile label-free and enzyme-free omethoate detection platform has been successfully constructed through the interaction between split G4 with DNA-AgNCs.
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Affiliation(s)
- Li Yin
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Hui Zhang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ying Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Liang He
- Penglai Jiaxin Dye Chemical., LTD, Yantai 265600, China
| | - Lihua Lu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
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9
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Feng DQ, Liu G. Dual-Channel Logic Gates Operating on the Chemopalette ssDNA-Ag NCs/GO Nanocomposites. Anal Chem 2021; 93:8326-8335. [PMID: 34076403 DOI: 10.1021/acs.analchem.1c01288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work, we demonstrate that the emission wavelength and intensity of silver nanoclusters (Ag NCs) can be facilely tuned by the configuration transformation from the adsorption of Ag NCs to the graphene oxide (GO) surface to the desorption of Ag NCs from GO. Bicolor Ag NCs tethering the complementary sequence of influenza A virus genes are prepared, named green-emitting G-Ag NCs-CH5N1 (530 nm) and red-emitting R-Ag NCs-CH1N1 (589 nm). As for the high affinity of the complementary fragment of genes to GO, the adsorption of Ag NCs to GO leads to the formation of G-Ag NCs-CH5N1/GO and R-Ag NCs-CH1N1/GO nanocomposites, leading to fluorescent quenching due to energy transfer. By conjugating complementary sequences as capturing probes for targets, the formation of genes/Ag NC duplex-stranded structures results in the desorption of Ag NCs from GO, activating the fluorescence signal. More interestingly, compared with sole single-stranded DNA-templated fluorescent Ag NCs (ssDNA-Ag NCs), the activatable emission wavelength of the G-Ag NCs-CH5N1/H5N1 complex exhibits a notable red shift (555 nm) with a 49% recovery rate, while that of the R-Ag NCs-CH1N1/H1N1 complex shows a distinct blue shift (569 nm) with a 200% recovery rate. Via target-responsive configuration transformation of Ag NCs/GO hybrid materials, the emission wavelength and intensity of Ag NCs are effectively regulated. Based on the output changes according to different input combinations, novel dual-channel logic gates for multiplex simultaneous detection are developed by using the tunable color and intensity of ssDNA-Ag NCs. Our observation may open a new path for multiplex analysis in a facile and rapid way combining the logic gate strategy.
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Affiliation(s)
- Da-Qian Feng
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Guoliang Liu
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, China
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10
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Qiao Z, Zhang J, Hai X, Yan Y, Song W, Bi S. Recent advances in templated synthesis of metal nanoclusters and their applications in biosensing, bioimaging and theranostics. Biosens Bioelectron 2021; 176:112898. [PMID: 33358287 DOI: 10.1016/j.bios.2020.112898] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/03/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022]
Abstract
As a kind of promising nanomaterials, metal nanoclusters (MNCs) generally composed of several to hundreds of metal atoms have received increasing interest owing to their unique properties, such as ultrasmall size (<2 nm), fascinating physical and chemical properties, and so on. Recently, template-assisted synthesis of MNCs (e.g., Au, Ag, Cu, Pt and Cd) has attracted extensive attention in biological fields. Up to now, various templates (e.g., dendrimers, polymers, DNAs, proteins and peptides) with different configurations and spaces have been applied to prepare MNCs with the advantages of facile preparation, controllable size, good water-solubility and biocompatibility. Herein, we focus on the recent advances in the template-assisted synthesis of MNCs, including the templates used to synthesize MNCs, and their applications in biosensing, bioimaging, and disease theranostics. Finally, the challenges and future perspectives of template-assisted synthesized MNCs are highlighted. We believe that this review could not only arouse more interest in MNCs but also promote their further development and applications by presenting the recent advances in this area to researchers from various fields, such as chemistry, material science, physiology, biomedicine, and so on.
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Affiliation(s)
- Zhenjie Qiao
- Research Center for Intelligent and Wearable Technology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, PR China
| | - Jian Zhang
- Research Center for Intelligent and Wearable Technology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, PR China
| | - Xin Hai
- Research Center for Intelligent and Wearable Technology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, PR China
| | - Yongcun Yan
- Research Center for Intelligent and Wearable Technology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, PR China
| | - Weiling Song
- Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Sai Bi
- Research Center for Intelligent and Wearable Technology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, PR China.
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11
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de la Hoz A, Navarro A, Aviñó A, Eritja R, Gargallo R. Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences. RSC Adv 2021; 11:9029-9042. [PMID: 35423401 PMCID: PMC8695332 DOI: 10.1039/d1ra00194a] [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: 01/09/2021] [Accepted: 02/15/2021] [Indexed: 12/22/2022] Open
Abstract
Silver nanoclusters (AgNCs) prepared by the reduction of silver ions in the presence of DNA oligonucleotides have attracted great interest as potential diagnostic tools for their tunable and high fluorescent properties. In this work, three DNA sequences that consist of a 12-nucleotide long probe sequence at the 5′-end linked to the complementary sequence to three miRNAs are studied. First, the interaction of these sequences with Ag(i) was characterized by means of circular dichroism spectroscopy. By applying multivariate methods to the analysis of spectroscopic data, two complexes with different Ag(i) : DNA ratios were resolved. Secondly, the impact of several experimental variables, such as temperature, borohydride concentration and reaction time, on the formation of AgNCs templated by these three sequences was studied. Finally, the fluorescence properties of the duplexes formed by DNA probes with complementary DNA or miRNA sequences were studied. The results presented here highlight the role of the secondary structure adopted by the DNA probe on the fluorescence properties of DNA-stabilized AgNCs which, in turn, affect the development of methods for miRNA detection. Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.![]()
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Affiliation(s)
- Alejandra de la Hoz
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
| | - Alba Navarro
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN Jordi Girona 18-26 E-08034 Barcelona Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN Jordi Girona 18-26 E-08034 Barcelona Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona Marti i Franquès 1 E-08028 Barcelona Spain
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12
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Ma J, Niu H, Gu S. The spatial organization of trace silver atoms on a DNA template. RSC Adv 2020; 11:1153-1163. [PMID: 35423706 PMCID: PMC8693506 DOI: 10.1039/d0ra08066g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
DNA with programmable information can be used to encode the spatial organization of silver atoms. Based on the primary structures of a DNA template containing a controllable base arrangement and number, the surrounding environment and cluster together can induce the folding of the DNA template into an appropriate secondary structure for forming AgNCs with different fluorescence emissions, such as i-motif, G-quadruplex, dimeric template, triplex, monomeric or dimeric C-loop, emitter pair, and G-enhancer/template conjugate. Stimuli can induce the dynamic structural transformation of the DNA template with a recognition site for favourably or unfavourably forming AgNCs, along with varied fluorescence intensities and colours. The array of several or more of the same and different clusters can be performed on simple and complex nanostructures, while maintaining their original properties. By sorting out this review, we systematically conclude the link between the performance of AgNCs and the secondary structure of the DNA template, and summarize the precise arrangement of nanoclusters on DNA nanotechnology. This clear review on the origin and controllability of AgNCs based on the secondary structure of the DNA template is beneficial for exploring the new probe and optical devices.
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Affiliation(s)
- Jinliang Ma
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127 China
| | - Huawei Niu
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology Luoyang Henan 471023 China
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Yang M, Chen X, Su Y, Liu H, Zhang H, Li X, Xu W. The Fluorescent Palette of DNA-Templated Silver Nanoclusters for Biological Applications. Front Chem 2020; 8:601621. [PMID: 33262973 PMCID: PMC7686567 DOI: 10.3389/fchem.2020.601621] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Recently years have witnessed a surge in application of DNA-AgNCs in optics, catalysis, sensing, and biomedicine. DNA-templated silver nanoclusters (DNA-AgNCs), as emerging fluorophores, display superior optical performance since their size is close to the Fermi wavelength. DNA-AgNCs possess unique features, including high fluorescence quantum yields and stability, biocompatibility, facile synthesis, and low toxicity, which are requisite for fluorescent probes. The fluorescent emission of DNA-AgNCs can cover the violet to near-infrared (NIR) region by varying the DNA sequences, lengths, and structures or by modifying the environmental factors (such as buffer, pH, metal ions, macromolecular polymers, and small molecules). In view of the above excellent properties, we overview the DNA-AgNCs from the viewpoints of synthesis and fluorescence properties, and summarized its biological applications of fluorescence sensing and imaging.
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Affiliation(s)
- Min Yang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Xu Chen
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
| | - Yuan Su
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
| | - Haiyan Liu
- Faculty of Public Health, North China University of Technology, Tangshan, China
| | - Hongxing Zhang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Xiangyang Li
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Wentao Xu
- Institute of Nutrition and Health, China Agricultural University, Beijing, China
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Base amount-dependent fluorescence enhancement for the assay of vascular endothelial growth factor 165 in human serum using hairpin DNA-silver nanoclusters and oxidized carbon nanoparticles. Mikrochim Acta 2020; 187:629. [PMID: 33123813 DOI: 10.1007/s00604-020-04592-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/07/2020] [Indexed: 10/23/2022]
Abstract
A base amount-dependent fluorescence enhancement-based strategy is put forward to determine vascular endothelial growth factor 165 (VEGF165) in human serum by the use of hairpin DNA-silver nanoclusters (hDNA-AgNCs) and oxidized carbon nanoparticles (CNPs). The hDNA-AgNCs aptasensing probe consists of AgNCs-contained hairpin loop (that generates a fluorescence signal), hairpin stem (that makes the structure stable), and the terminal aptamer 1 (that recognizes the target together with aptamer 2). It has been demonstrated that the fluorescence intensity of hDNA-AgNCs is ~ 3-fold stronger than that of single-stranded DNA-AgNCs (ssDNA-AgNCs), and hDNA-AgNCs have a strong dependence of fluorescence enhancement on the base amount in hairpin stem and loop. Upon the addition of oxidized CNPs, the terminal aptamer 1 of hDNA-AgNCs can adsorb onto the surface of oxidized CNPs via π-π stacking, and the fluorescence of hDNA-AgNCs (with excitation/emission maxima at 490/567 nm) is quenched via fluorescence resonance energy transfer (FRET). When aptamer 2 and VEGF165 are subsequently added, aptamer 1, VEGF165, and aptamer 2 reassemble into an intact tertiary structure, and the fluorescence is recovered because hDNA-AgNCs are far away from the surface of oxidized CNPs and the FRET efficiency decreases. Under the optimized conditions, the aptasensing probe can selectively assay VEGF165 with a detection limit of 14 pM. The results provide a label-free and sensitive method to monitor VEGF165 in human serum. Schematic representation of the strong dependence of fluorescence enhancement on base amount in stem and loop of hairpin DNA-silver nanoclusters. The probe can be used to assay vascular endothelial growth factor 165 (VEGF165) and give a judgment whether human serum VEGF165 is at a normal or abnormal level for clinical diagnosis.
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Shah P, Nagda R, Jung IL, Bhang YJ, Jeon SW, Lee CS, Do C, Nam K, Kim YM, Park S, Roh YH, Thulstrup PW, Bjerrum MJ, Kim TH, Yang SW. Noncanonical Head-to-Head Hairpin DNA Dimerization Is Essential for the Synthesis of Orange Emissive Silver Nanoclusters. ACS NANO 2020; 14:8697-8706. [PMID: 32525298 DOI: 10.1021/acsnano.0c03095] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA secondary structures, such as dimers and hairpins, are important for the synthesis of DNA template-embedded silver nanoclusters (DNA/AgNCs). However, the arrangement of AgNCs within a given DNA template and how the AgNC influences the secondary structure of the DNA template are still unclear. Here, we introduce a noncanonical head-to-head hairpin DNA nanostructure that is driven by orange-emissive AgNCs. Through detailed in-gel analysis, sugar backbone switching, inductively coupled plasma mass spectrometry, small-angle X-ray scattering, and small angle neutron scattering, we show that the orange-emissive AgNCs mediate cytosine-Ag-cytosine bridging between two six-cytosine loop (6C-loop) hairpin DNA templates. Unlike green, red, or far-red emissive AgNCs, which are embedded inside a hairpin and duplex DNA template, the orange-emissive AgNCs are localized on the interface between the two 6C-loop hairpin DNA templates, thereby linking them. Moreover, we found that deoxyribose in the backbone of the 6C-loop at the third and fourth cytosines is crucial for the formation of the orange-emissive AgNCs and the head-to-head hairpin DNA structure. Taken together, we suggest that the specific wavelength of AgNCs fluorescence is determined by the mutual interaction between the secondary or tertiary structures of DNA- and AgNC-mediated intermolecular DNA cross-linking.
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Affiliation(s)
- Pratik Shah
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Riddhi Nagda
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Il Lae Jung
- Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon 34057, Korea
| | - Yong Joo Bhang
- Seoulin Bioscience Co. Ltd., 4F. #A, KOREA BIO PARK, 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Korea
| | - Sang-Woo Jeon
- Department of Quantum System Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, 54896, Korea
| | - Chang Seop Lee
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Changwoo Do
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Sooyeon Park
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Peter Waaben Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
| | - Morten Jannik Bjerrum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
| | - Tae-Hwan Kim
- Department of Quantum System Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, 54896, Korea
| | - Seong Wook Yang
- Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Copenhagen 2000, Denmark
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16
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Geczy R, Christensen NJ, Rasmussen KK, Kálomista I, Tiwari MK, Shah P, Yang SW, Bjerrum MJ, Thulstrup PW. Formation and Structure of Fluorescent Silver Nanoclusters at Interfacial Binding Sites Facilitating Oligomerization of DNA Hairpins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Reka Geczy
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Niels Johan Christensen
- Department of Chemistry University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kim K. Rasmussen
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Ildikó Kálomista
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Manish K. Tiwari
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Pratik Shah
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Seong Wook Yang
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Morten J. Bjerrum
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Peter W. Thulstrup
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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17
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Geczy R, Christensen NJ, Rasmussen KK, Kálomista I, Tiwari MK, Shah P, Yang SW, Bjerrum MJ, Thulstrup PW. Formation and Structure of Fluorescent Silver Nanoclusters at Interfacial Binding Sites Facilitating Oligomerization of DNA Hairpins. Angew Chem Int Ed Engl 2020; 59:16091-16097. [DOI: 10.1002/anie.202005102] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/18/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Reka Geczy
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Niels Johan Christensen
- Department of Chemistry University of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kim K. Rasmussen
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Ildikó Kálomista
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Manish K. Tiwari
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Pratik Shah
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Seong Wook Yang
- Department of Systems Biology Institute of Life Science and Biotechnology Yonsei University Seoul 03722 Korea
| | - Morten J. Bjerrum
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
| | - Peter W. Thulstrup
- Department of Chemistry University of Copenhagen Universitetsparken 5 2100 Copenhagen Denmark
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18
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He J, Zhang Y, Chen Z, Li C, Yuan R, Xu W. Targeted DNA-driven catalytic assembly light-up ratiometric fluorescence of biemissive silver nanoclusters for amplified biosensing. Chem Commun (Camb) 2020; 56:10325-10328. [DOI: 10.1039/d0cc04055j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a ratiometric fluorescence strategy using biemissive silver nanoclusters that are harbored in a functional hairpin beacon for rapid, specific and sensitive detection of specific HIV-related DNA as a model.
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Affiliation(s)
- Jiayang He
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yuxuan Zhang
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Zehui Chen
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Chong Li
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Wenju Xu
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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Structural Influence on the Post-Clustering Stability of DNA/AgNCs Fluorescence. NANOMATERIALS 2019; 9:nano9050667. [PMID: 31035341 PMCID: PMC6566520 DOI: 10.3390/nano9050667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 04/24/2019] [Indexed: 01/28/2023]
Abstract
DNA-encapsulated Silver Nanoclusters (DNA/AgNCs) based sensors have gained increasing attention in past years due to their diverse applications in bioimaging, biosensing, and enzymatic assays. Given the potential of DNA/AgNCs for practical applications, the systematic studies of the fluorescent stability over an extended period is necessary. However, the correlation between nucleic acid properties and the long-term stability of DNA/AgNCs is less known. With locking-to-unlocking sensors, in which the secondary structure of DNA template is standardized, we investigated the correlation between the DNA structure and the fluorescence stability of AgNCs. Post-synthesis of DNA/AgNCs, the fluorescence, and structures of templates were monitored over three weeks. By combining the fluorescence spectroscopy with the in-gel fluorescent assay, we found that AgNCs encapsulated by dimer-structured DNA/AgNCs templates were more stable than those of hairpin-structured DNA/AgNCs templates. While the orange fluorescence from the dimer templates increased over three weeks, the red fluorescence from the hairpin templates was diminished by >80% within two days at room temperature. Further tests revealed that hairpin-encapsulated red-emissive AgNCs is more sensitive to oxidation by atmospheric oxygen compared to dimer encapsulated orange AgNCs. Our observations may provide an important clue in encapsulating photophysically more stable AgNCs by tuning the DNA secondary structures. The proposed strategy here can be essential for pragmatic applications of DNA/AgNCs templates.
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