1
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Copp SM, Gonzàlez-Rosell A. Large-scale investigation of the effects of nucleobase sequence on fluorescence excitation and Stokes shifts of DNA-stabilized silver clusters. NANOSCALE 2021; 13:4602-4613. [PMID: 33605954 PMCID: PMC8043073 DOI: 10.1039/d0nr08300c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
DNA-stabilized silver clusters (AgN-DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the understanding of AgN-DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most AgN-DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of AgN-DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 AgN-DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive AgN-DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects AgN-DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in AgN-DNAs, and discuss how differences in AgN-DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in AgN-DNAs and the relations of this process to AgN-DNA structure.
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Affiliation(s)
- Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2585, USA. and Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA and Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-2580, USA
| | - Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2585, USA.
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2
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Wang Y, Wei Y, Zhang Y, Wang L, Dong Y. Enzyme-free and DNA-based universal platform for the construction of various logic devices based on graphene oxide and G-quadruplex. Comput Biol Chem 2020; 89:107374. [PMID: 32987286 DOI: 10.1016/j.compbiolchem.2020.107374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/22/2020] [Accepted: 09/10/2020] [Indexed: 11/16/2022]
Abstract
In the fields of biocomputing and biomolecular, DNA molecules are applicable to be regarded as data of logical computing platform that uses elaborate logic gates to perform a variety of tasks. Graphene oxide (GO) is a type of novel nanomaterial, which brings new research focus to materials science and biosensors due to its special selectivity and excellent quenching ability. G-quadruplex as a unique DNA structure stimulates the intelligent application of DNA assembly on the strength of its exceptional binding activity. In this paper, we report a universal logic device assisted with GO and G-quadruplex under an enzyme-free condition. Integrated with the quenching ability of GO to the TAMRA (fluorophore, Carboxytetramethylrhodamine) and the enhancement of fluorescence intensity produced by the peculiar binding of G-quadruplex to the NMM (N-methylmesoporphyrin IX), a series of basic binary logic gates (AND. OR. INHIBIT. XOR) have been designed and verified through biological experiments. Given the modularity and programmability of this strategy, two advanced logic gates (half adder and half subtractor) were realized on the basis of the same work platform. The fluorescence signals generated from different input combinations possessed satisfactory results, which provided proof of feasibility. We believe that the proposed universal logical platform that operates at the nanoscale is expected to be utilized for future applications in molecular computing as well as disease diagnosis.
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Affiliation(s)
- Yue Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Yani Wei
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yingying Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Luhui Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yafei Dong
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China; College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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3
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Lv M, Zhou W, Fan D, Guo Y, Zhu X, Ren J, Wang E. Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA-Templated Silver Nanoclusters as Universal Dual-Output Generators. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1908480. [PMID: 32196133 DOI: 10.1002/adma.201908480] [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] [Received: 01/08/2020] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 05/21/2023]
Abstract
Exquisite administration of a new type of hairpin DNA-templated silver nanoclusters (H-AgNCs) as universal dual-output generators in DNA-based logic systems is reported. Diverse concomitant contrary logic gates (CCLGs) with opposite functions (YES^ NOT, OR^ NOR, INHIBIT^ IMPLICATION, XOR^ XNOR, and MAJORITY^ MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and improves repeatability of operation, but also makes it convenient to connect distinct DNA-based logic gates. It is worthy to anticipate that the cost-effective strategy will inspire researchers to develop much more complex logic systems and contribute to the field of molecular computing.
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Affiliation(s)
- Mengmeng Lv
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weijun Zhou
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Daoqing Fan
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yuchun Guo
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
| | - Xiaoqing Zhu
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jiangtao Ren
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Erkang Wang
- Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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4
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Wang Y, Lv Q, Zhang Y, Wang L, Dong Y. Probe computing model based on small molecular switch. BMC Bioinformatics 2019; 20:285. [PMID: 31182004 PMCID: PMC6557740 DOI: 10.1186/s12859-019-2767-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA has been widely used to construct the advanced logic devices. Results Herein, a molecular probe apparatus was constructed based on DNA molecular computing to perform fluorescent quenching and fluorescent signal recovery, with an ’ ON/OFF’ switching function. In this study, firstly, we program the streptavidin-mediated fluorescent quenching apparatus based on short-distance strand migration. The variation of fluorescent signal is acted as output. Then DNAzyme as a switching controller was involved to regulate the fluorescent signal increase. Finally, on this base, a cascade DNA logic gate consists of two logic AND operations was developed to enrich probe machine. Conclusion The designed probe computing model can be implemented with readout of fluorescence intensity, and exhibits great potential applications in the field of bioimaging as well as disease diagnosis.
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5
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Suo Z, Chen J, Hou X, Hu Z, Xing F, Feng L. Growing prospects of DNA nanomaterials in novel biomedical applications. RSC Adv 2019; 9:16479-16491. [PMID: 35516377 PMCID: PMC9064466 DOI: 10.1039/c9ra01261c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.
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Affiliation(s)
- Zhiguang Suo
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Jingqi Chen
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Xialing Hou
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Ziheng Hu
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Feifei Xing
- Department of Chemistry, College of Science, Shanghai University Shanghai 200444 China
| | - Lingyan Feng
- Materials Genome Institute, Shanghai University Shanghai 200444 China
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Zhang X, Chen L, Lim KH, Gonuguntla S, Lim KW, Pranantyo D, Yong WP, Yam WJT, Low Z, Teo WJ, Nien HP, Loh QW, Soh S. The Pathway to Intelligence: Using Stimuli-Responsive Materials as Building Blocks for Constructing Smart and Functional Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1804540. [PMID: 30624820 DOI: 10.1002/adma.201804540] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/09/2018] [Indexed: 05/22/2023]
Abstract
Systems that are intelligent have the ability to sense their surroundings, analyze, and respond accordingly. In nature, many biological systems are considered intelligent (e.g., humans, animals, and cells). For man-made systems, artificial intelligence is achieved by massively sophisticated electronic machines (e.g., computers and robots operated by advanced algorithms). On the other hand, freestanding materials (i.e., not tethered to a power supply) are usually passive and static. Hence, herein, the question is asked: can materials be fabricated so that they are intelligent? One promising approach is to use stimuli-responsive materials; these "smart" materials use the energy supplied by a stimulus available from the surrounding for performing a corresponding action. After decades of research, many interesting stimuli-responsive materials that can sense and perform smart functions have been developed. Classes of functions discussed include practical functions (e.g., targeting and motion), regulatory functions (e.g., self-regulation and amplification), and analytical processing functions (e.g., memory and computing). The pathway toward creating truly intelligent materials can involve incorporating a combination of these different types of functions into a single integrated system by using stimuli-responsive materials as the basic building blocks.
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Affiliation(s)
- Xuan Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Linfeng Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Hui Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Spandhana Gonuguntla
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Kang Wen Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Dicky Pranantyo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wai Pong Yong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wei Jian Tyler Yam
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Zhida Low
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Wee Joon Teo
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Hao Ping Nien
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Qiao Wen Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
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7
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Yang S, Yang C, Huang D, Song L, Chen J, Yang Q. Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits. Chemistry 2019; 25:5389-5405. [PMID: 30328639 DOI: 10.1002/chem.201804420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Indexed: 01/06/2023]
Abstract
DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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8
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Tregubov AA, Nikitin PI, Nikitin MP. Advanced Smart Nanomaterials with Integrated Logic-Gating and Biocomputing: Dawn of Theranostic Nanorobots. Chem Rev 2018; 118:10294-10348. [DOI: 10.1021/acs.chemrev.8b00198] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Andrey A. Tregubov
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, Moscow 119991, Russia
| | - Maxim P. Nikitin
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
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9
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Ran X, Wang Z, Ju E, Pu F, Song Y, Ren J, Qu X. An intelligent 1:2 demultiplexer as an intracellular theranostic device based on DNA/Ag cluster-gated nanovehicles. NANOTECHNOLOGY 2018; 29:065501. [PMID: 29226844 DOI: 10.1088/1361-6528/aaa09a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The logic device demultiplexer can convey a single input signal into one of multiple output channels. The choice of the output channel is controlled by a selector. Several molecules and biomolecules have been used to mimic the function of a demultiplexer. However, the practical application of logic devices still remains a big challenge. Herein, we design and construct an intelligent 1:2 demultiplexer as a theranostic device based on azobenzene (azo)-modified and DNA/Ag cluster-gated nanovehicles. The configuration of azo and the conformation of the DNA ensemble can be regulated by light irradiation and pH, respectively. The demultiplexer which uses light as the input and acid as the selector can emit red fluorescence or a release drug under different conditions. Depending on different cells, the intelligent logic device can select the mode of cellular imaging in healthy cells or tumor therapy in tumor cells. The study incorporates the logic gate with the theranostic device, paving the way for tangible applications of logic gates in the future.
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Affiliation(s)
- Xiang Ran
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, People's Republic of China. School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, People's Republic of China
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10
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Chen Z, Liu C, Cao F, Ren J, Qu X. DNA metallization: principles, methods, structures, and applications. Chem Soc Rev 2018; 47:4017-4072. [DOI: 10.1039/c8cs00011e] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.
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Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
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11
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Pu F, Ren J, Qu X. Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials. Chem Soc Rev 2017; 47:1285-1306. [PMID: 29265140 DOI: 10.1039/c7cs00673j] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.
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Affiliation(s)
- Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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12
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Ge L, Sun X, Hong Q, Li F. Ratiometric Catalyzed-Assembly of NanoCluster Beacons: A Nonenzymatic Approach for Amplified DNA Detection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:32089-32096. [PMID: 28849916 DOI: 10.1021/acsami.7b09034] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work, a novel fluorescent transformation phenomenon of oligonucleotide-encapsulated silver nanoclusters (AgNCs) was demonstrated, in which green-emissive AgNCs effectively transformed to red-emissive AgNCs when placed in close proximity to a special DNA fragment (denoted as convertor here). Taking advantage of a catalyzed-hairpin-assembly (CHA) amplification strategy, we rationally and compatibly engineered a simple and sensitive AgNC-based fluorescent signal amplification strategy through the ratiometric catalyzed-assembly (RCA) of green-emissive NanoCluster Beacon (NCB) with a convertor modified DNA hairpin to induce the template transformation circularly. The proposed ratiometric fluorescent biosensing platform based on RCA-amplified NCB (RCA-NCB) emits intense green fluorescence in the absence of target DNA and will undergo consecutively fluorescent signal transformation from green emission to red emission upon exposure to its target DNA. The ratiometric adaptation of the NCB to CHA circuit advances their general usability as biosensing platform with great improvements in detection sensitivity. By measuring the fluorescence intensity ratio of the red emission and green emission, the proposed RCA-NCB platform exhibits sensitive and accurate analytical performance toward Werner Syndrome-relevant gene, the proof-of-concept target in this work. A low detection limit down to the pM level was achieved, which is lower than most of the reported AgNC-based fluorescent DNA biosensors, making the proposed RCA-NCB biosensing strategy appealing in amplifying the ratiometric fluorescent signal for sensitive DNA detection. Moreover, our proposed RCA-NCB platform shows good recovery toward the target DNA in real human serum samples, illustrating their potential promise for clinical and imaging applications in the future.
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Affiliation(s)
- Lei Ge
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, 266109, People's Republic of China
| | - Ximei Sun
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, 266109, People's Republic of China
| | - Qing Hong
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao, 266109, People's Republic of China
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13
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Lin R, Tao G, Chen Y, Chen M, Liu F, Li N. Constructing a Robust Fluorescent DNA-Stabilized Silver Nanocluster Probe Module by Attaching a Duplex Moiety. Chemistry 2017; 23:10893-10900. [PMID: 28510342 DOI: 10.1002/chem.201701879] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Indexed: 12/16/2022]
Abstract
Fluorescent DNA-templated silver nanoclusters (DNA-Ag NCs) have served as excellent luminescent probes and operation units in various applications. However, the fluorescence property of DNA-Ag NCs is very sensitive to elongation or modification of the DNA template, limiting the breadth of applications. In this work, we propose a strategy for constructing a robust fluorescent DNA-Ag NCs probe module by attaching a duplex moiety to the nanocluster-bearing sequence. The fluorescence intensity of the DNA-Ag NCs can be enhanced 90-fold upon hybridization of the elongated moiety. Adenine in the linker sequence has a further enhancing effect on the fluorescence intensity, whereas thymine has a quenching effect. The transformation from a non-fluorescent species to fluorescent nanoclusters is responsible for the fluorescence enhancement with duplex formation of the elongated moiety. We hope that this design will aid future diversification of experimental designs to facilitate more applications that are currently limited by the aforementioned problems.
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Affiliation(s)
- Ruoyun Lin
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Yang Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Mingxing Chen
- Medium Instrument Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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14
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User Authorization at the Molecular Scale. Chemphyschem 2017; 18:1678-1687. [DOI: 10.1002/cphc.201700506] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/01/2017] [Indexed: 12/31/2022]
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15
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Ge L, Sun X, Hong Q, Li F. Ratiometric NanoCluster Beacon: A Label-Free and Sensitive Fluorescent DNA Detection Platform. ACS APPLIED MATERIALS & INTERFACES 2017; 9:13102-13110. [PMID: 28367619 DOI: 10.1021/acsami.7b03198] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Although researches until now have emphasized the influence of an oligonucleotide sequence on the fluorescence of oligonucleotide-stabilized silver nanoclusters (AgNCs), this influence has been explored as a novel ratiometric fluorescent signal transduction in this work. This study builds on our original discovery of a template-transformation phenomenon, which demonstrated that the connection of a special DNA fragment (5'-CACCGCTTT-3') with a green-emitting AgNC nucleation sequence (GNuS, 5'-TGCCTTTTGGGGACGGATA-3') creates a red-emitting AgNC nucleation sequence (RNuS, 5'-CACCGCTTTTGCCTTTTGGGGACGGATA-3'). Attempts to expand this idea and construct elegant ratiometric NanoCluster Beacons (NCBs) for DNA sequence detection are not straightforward, and, thus, we carried out a series of investigations with the goal of understanding the mechanism of this template-transformation phenomenon. Experimental results showed that the six-nucleotide fragment (5'-CACCGC-3') at the 5'-end of RNuS acts as a template convertor and takes full responsibility for the template transformation from GNuS to RNuS. Moreover, we found that the appropriate proximity of the convertor to GNuS also plays a significant role in the template transformation. We then show that the insights gained here for the template-transformation mechanism allow us to construct ratiometric NCBs by simply appending the convertor and the GNuS onto a rationally designed stem-loop probe. This new type of NCB emits intense red fluorescence without the addition of a target DNA and emerges as a new, bright green emission only when hybridized to its target DNA. By measuring the distinct variation in the fluorescence intensity ratios of green and red emission, this ratiometric NCB was demonstrated to sensitively detect Hepatitis-A virus gene sequences, a proof-of-concept target in this work, with good selectivity.
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Affiliation(s)
- Lei Ge
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao 266109, P. R. China
| | - Ximei Sun
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao 266109, P. R. China
| | - Qing Hong
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University , Qingdao 266109, P. R. China
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16
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Chen Y, Sun Y, Song R, Song S, Zhao Y, Yang X, Yu C, Lin Q. Fluorometric “Turn-On” glucose sensing through the in situ generation of silver nanoclusters. RSC Adv 2017. [DOI: 10.1039/c6ra26303h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A fluorometric “turn-on” glucose detection is performed based on the Fenton reaction which can trigger the generation of Ag nanoclusters.
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Affiliation(s)
- Yang Chen
- College of Science
- Northeast Forestry University
- Harbin
- P. R. China
| | - Yuanqing Sun
- College of Science
- Northeast Forestry University
- Harbin
- P. R. China
- State Key Laboratory of Supramolecular Structure and Materials
| | - Rongjun Song
- College of Science
- Northeast Forestry University
- Harbin
- P. R. China
| | - Shanliang Song
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun
- P. R. China
| | - Yue Zhao
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun
- P. R. China
| | - Xudong Yang
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun
- P. R. China
| | - Cong Yu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Quan Lin
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun
- P. R. China
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17
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New SY, Lee ST, Su XD. DNA-templated silver nanoclusters: structural correlation and fluorescence modulation. NANOSCALE 2016; 8:17729-17746. [PMID: 27722695 DOI: 10.1039/c6nr05872h] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
12 years after the introduction of DNA-templated silver nanoclusters (DNA-AgNCs), exciting progress has been made and yet we are still in the midst of trying to fully understand this nanomaterial. The prominent excellence of DNA-AgNCs is undoubtedly its modulatable emission property, of which how variation in DNA templates causes emission tuning remains elusive. Based on the up-to-date DNA-AgNCs, we aim to establish the correlation between the structure/sequence of DNA templates and emission behaviour of AgNCs. Herein, we systematically present a wide-range of DNA-AgNCs based on the structural complexity of the DNA templates, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), triple-stranded DNA (tsDNA) and DNA nanostructures. For each DNA category, we discuss the emission property, quantum yield and synthesis condition of the respective AgNCs, before cross-comparing the impact of different DNA scaffolds on the properties of AgNCs. A future outlook for this area is given as a conclusion. By putting the information together, this review may shed new light on understanding DNA-AgNCs while we are expecting continuous breakthroughs in this field.
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Affiliation(s)
- S Y New
- School of Pharmacy, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - S T Lee
- School of Pharmacy, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - X D Su
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Singapore 138634.
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18
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Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform. Sci Rep 2016; 6:34810. [PMID: 27713517 PMCID: PMC5054380 DOI: 10.1038/srep34810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/20/2016] [Indexed: 01/16/2023] Open
Abstract
A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.
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19
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Copp SM, Schultz D, Swasey SM, Faris A, Gwinn EG. Cluster Plasmonics: Dielectric and Shape Effects on DNA-Stabilized Silver Clusters. NANO LETTERS 2016; 16:3594-9. [PMID: 27187492 DOI: 10.1021/acs.nanolett.6b00723] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This work investigates the effects of dielectric environment and cluster shape on electronic excitations of fluorescent DNA-stabilized silver clusters, AgN-DNA. We first establish that the longitudinal plasmon wavelengths predicted by classical Mie-Gans (MG) theory agree with previous quantum calculations for excitation wavelengths of linear silver atom chains, even for clusters of just a few atoms. Application of MG theory to AgN-DNA with 400-850 nm cluster excitation wavelengths indicates that these clusters are characterized by a collective excitation process and suggests effective cluster thicknesses of ∼2 silver atoms and aspect ratios of 1.5 to 5. To investigate sensitivity to the surrounding medium, we measure the wavelength shifts produced by addition of glycerol. These are smaller than reported for much larger gold nanoparticles but easily detectable due to narrower line widths, suggesting that AgN-DNA may have potential for fluorescence-reported changes in dielectric environment at length scales of ∼1 nm.
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Affiliation(s)
- Stacy M Copp
- Department of Physics, University of California , Santa Barbara, California 93106-9530, United States
| | - Danielle Schultz
- Department of Chemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Steven M Swasey
- Department of Chemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Alexis Faris
- Department of Physics, University of California , Santa Barbara, California 93106-9530, United States
| | - Elisabeth G Gwinn
- Department of Physics, University of California , Santa Barbara, California 93106-9530, United States
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20
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Tao Y, Li M, Ren J, Qu X. Metal nanoclusters: novel probes for diagnostic and therapeutic applications. Chem Soc Rev 2016; 44:8636-63. [PMID: 26400655 DOI: 10.1039/c5cs00607d] [Citation(s) in RCA: 481] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal nanoclusters, composed of several to a few hundred metal atoms, have received worldwide attention due to their extraordinary physical and chemical characteristics. Recently, great efforts have been devoted to the exploration of the potential diagnostic and therapeutic applications of metal nanoclusters. Here we focus on the recent advances and new horizons in this area, and introduce the rising progress on the use of metal nanoclusters for biological analysis, biological imaging, therapeutic applications, DNA assembly and logic gate construction, enzyme mimic catalysis, as well as thermometers and pH meters. Furthermore, the future challenges in the construction of biofunctional metal nanoclusters for diagnostic and therapeutic applications are also discussed. We expect that the rapidly growing interest in metal nanocluster-based theranostic applications will certainly not only fuel the excitement and stimulate research in this highly active field, but also inspire broader concerns across various disciplines.
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Affiliation(s)
- Yu Tao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mingqiang Li
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
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21
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Fan D, Zhu J, Liu Y, Wang E, Dong S. Label-free and enzyme-free platform for the construction of advanced DNA logic devices based on the assembly of graphene oxide and DNA-templated AgNCs. NANOSCALE 2016; 8:3834-3840. [PMID: 26814682 DOI: 10.1039/c6nr00032k] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA-based molecular logic computation has drawn extensive attention in bioanalysis, intelligent diagnostics of diseases and other nanotechnology areas. Herein, taking 2-to-1 and 4-to-2 encoders and a 1-to-2 decoder as model molecular logic devices, we for the first time combined the quenching ability of GO (graphene oxide) to DNA-templated AgNCs with G-quadruplex-enhanced fluorescence intensity of porphyrin dyes for the construction of label-free and enzyme-free dual-output advanced DNA molecular logic devices. Also, through the application of negative logic conversion to an XOR logic gate and combined with an INHIBIT logic gate, we also operated a label-free and enzyme-free comparator.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
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22
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Xing Y, Liu H, Yu W. Preparation and characterization of keratin and chicken egg white-templated luminescent Au cluster composite film. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Chen J, Ji X, Tinnefeld P, He Z. Multifunctional Dumbbell-Shaped DNA-Templated Selective Formation of Fluorescent Silver Nanoclusters or Copper Nanoparticles for Sensitive Detection of Biomolecules. ACS APPLIED MATERIALS & INTERFACES 2016; 8:1786-94. [PMID: 26719979 DOI: 10.1021/acsami.5b09678] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In this work, a multifunctional template for selective formation of fluorescent silver nanoclusters (AgNCs) or copper nanoparticles (CuNPs) is put forward. This dumbbell-shaped (DS) DNA template is made up of two cytosine hairpin loops and an adenine-thymine-rich double-helical stem which is closed by the loops. The cytosine loops act as specific regions for the growth of AgNCs, and the double-helical stem serves as template for the CuNPs formation. By carefully investigating the sequence and length of DS DNA, we present the optimal design of the template. Benefiting from the smart design and facile synthesis, a simple, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection is proposed. Through the systematic comparison, it is found that the strategy based on CuNPs formation is more sensitive for ATP assay than that based on AgNCs synthesis, and the detection limitation was found to be 81 pM. What's more, the CuNPs formation-based method is successfully applied in the detection of ATP in human serum as well as the determination of cellular ATP. In addition to small target molecule, the sensing strategy was also extended to the detection of biomacromolecule (DNA), which illustrates the generality of this biosensor.
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Affiliation(s)
- Jinyang Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, People's Republic of China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, People's Republic of China
| | - Philip Tinnefeld
- NanoBioSciences Group, Institute for Physical and Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology , Braunschweig, 38106, Germany
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, People's Republic of China
- NanoBioSciences Group, Institute for Physical and Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology , Braunschweig, 38106, Germany
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24
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Zhang K, Wang K, Zhu X, Xie M, Xu F. A label-free kissing complex-induced fluorescence sensor for DNA and RNA detection by using DNA-templated silver nanoclusters as a signal transducer. RSC Adv 2016. [DOI: 10.1039/c6ra22515b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new strategy integrate silver nanoclusters (AgNCs) and riboswitches for the expanding of the application of a kissing complexes-induced sensor (KCIS) for the assay of DNA and RNA was reported.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Ke Wang
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Xue Zhu
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Minhao Xie
- Key Laboratory of Nuclear Medicine
- Ministry of Health
- Jiangsu Key Laboratory of Molecular Nuclear Medicine
- Jiangsu Institute of Nuclear Medicine
- Wuxi
| | - Fei Xu
- Department of Laboratory Medicine
- Wuxi Municipal Women and Children Health Hospital
- Wuxi
- China
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25
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Ran X, Wang Z, Zhang Z, Pu F, Ren J, Qu X. Nucleic-acid-programmed Ag-nanoclusters as a generic platform for visualization of latent fingerprints and exogenous substances. Chem Commun (Camb) 2016; 52:557-60. [DOI: 10.1039/c5cc08534a] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A nucleic acid controlled AgNC platform for simultaneous imaging and quantitative detection of substances in fingerprints.
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Affiliation(s)
- Xiang Ran
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Zhenzhen Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Zhijun Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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26
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Cao Q, Teng Y, Yang X, Wang J, Wang E. A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors. Biosens Bioelectron 2015; 74:318-21. [DOI: 10.1016/j.bios.2015.06.044] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 01/21/2023]
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27
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Zhang K, Wang K, Zhu X, Xie M. A label-free kissing complexes-induced fluorescence aptasensor using DNA-templated silver nanoclusters as a signal transducer. Biosens Bioelectron 2015; 78:154-159. [PMID: 26606306 DOI: 10.1016/j.bios.2015.11.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 01/20/2023]
Abstract
Riboswitches are complex folded RNA domains that serve as receptors for specific metabolites which identified in prokaryotes. They are comprised of a biosensor that includes the binding site for a small ligand and they respond to association with this ligand by undergoing a conformational change. In the present study, we report on the integration of silver nanoclusters (AgNCs) and riboswitches for the development of a kissing complexes-induced aptasensor (KCIA). We specifically apply the tunable riboswitches properties of this strategy to demonstrate the multiplexes analysis of adenosine and adenosine deaminase (ADA). This strategy allows for simple tethering of the specific oligonucleotides stabilizing the AgNCs to the nucleic acid probes. This is a new concept for aptasensors, and opens an opportunity for design of more novel biosensors based on the kissing complexes-induced strategy.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China.
| | - Ke Wang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Xue Zhu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Minhao Xie
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
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28
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Wang KH, Chang CW. The spectral relaxation dynamics and the molecular crowding effect of silver nanoclusters synthesized in the polymer scaffold. Phys Chem Chem Phys 2015; 17:23140-6. [PMID: 26279125 DOI: 10.1039/c5cp03175c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have performed a comprehensive study on the spectral relaxation dynamics of silver nanoclusters (AgNCs) synthesized in poly(methacrylic acid) (PMAA). In different polymer conformations and solvents, the spectral relaxation dynamics of PMAA-AgNCs can be globally fitted by a bi-exponential decay, the short component is about 0.2-0.3 ns, whereas the long component is in the range 1-3 ns. The spectral relaxation is associated with the energy transfer dynamics and the excitation of multiple emissive AgNCs. In this study, we have demonstrated the feasibility of using AgNCs as a fluorescent probe for fluorescence anisotropy studies. Meanwhile, the molecular crowding effects of the PMAA-AgNCs were addressed using the Triton X-100 reverse micelles. The results indicate that the fluorescence quantum yield of the AgNCs will be significantly increased under crowded conditions, which is beneficial for their usage in intracellular imaging studies.
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Affiliation(s)
- Kai-Hung Wang
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan.
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29
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Liu L, Liu C, Nie L, Jiang T, Hong J, Zhang X, Luo L, Wang X. Study on the synergistic antibacterial effect of silver-carried layered zirconium alkyl-N,N-dimethylenephosphonate. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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Shah P, Thulstrup PW, Cho SK, Bhang YJ, Ahn JC, Choi SW, Bjerrum MJ, Yang SW. In-solution multiplex miRNA detection using DNA-templated silver nanocluster probes. Analyst 2015; 139:2158-66. [PMID: 24616905 DOI: 10.1039/c3an02150e] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MicroRNAs (miRNAs) are small regulatory RNAs (size ∼21nt to ∼25nt) that can be used as biomarkers of disease diagnosis, and efforts have been directed towards the invention of a rapid, simple and sequence-selective detection method for miRNAs. We recently developed a DNA/silver nanoclusters (AgNCs)-based turn-off fluorescence method in the presence of target miRNA. To further advance our method toward multiplex miRNA detection in solution, the design of various fluorescent DNA/AgNCs probes was essential. Therefore, tethering of DNA-12nt scaffolds with 9 different AgNCs emitters to target-sensing DNA sequences was investigated. Interestingly, for the creation of spectrally different DNA/AgNCs probes, not only were the emitters encapsulated in 9 different DNA-12nt scaffolds necessary but the tethered target-sensing DNA sequences are also crucial to tune the fluorescence across the visible to infra-red region. In this study, we obtained three spectrally distinctive emitters of each DNA/AgNCs probes such as green, red, and near-infrared (NIR) fluorescence. Using these DNA/AgNCs probes, we here show a proof of concept for a rapid, one-step, in-solution multiplex miRNA detection method.
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Affiliation(s)
- Pratik Shah
- UNIK Center for Synthetic Biology/Plant Biochemistry Laboratory, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark.
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31
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Liu W, Lai H, Huang R, Zhao C, Wang Y, Weng X, Zhou X. DNA methyltransferase activity detection based on fluorescent silver nanocluster hairpin-shaped DNA probe with 5’-C-rich/G-rich-3’ tails. Biosens Bioelectron 2015; 68:736-740. [DOI: 10.1016/j.bios.2015.02.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/25/2015] [Accepted: 02/05/2015] [Indexed: 12/31/2022]
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32
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Chen J, Zhou S, Wen J. Concatenated Logic Circuits Based on a Three-Way DNA Junction: A Keypad-Lock Security System with Visible Readout and an Automatic Reset Function. Angew Chem Int Ed Engl 2014; 54:446-50. [DOI: 10.1002/anie.201408334] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/27/2014] [Indexed: 12/19/2022]
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33
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Chen J, Zhou S, Wen J. Concatenated Logic Circuits Based on a Three-Way DNA Junction: A Keypad-Lock Security System with Visible Readout and an Automatic Reset Function. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408334] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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34
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Copp SM, Bogdanov P, Debord M, Singh A, Gwinn E. Base motif recognition and design of DNA templates for fluorescent silver clusters by machine learning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:5839-45. [PMID: 25043854 DOI: 10.1002/adma.201401402] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/20/2014] [Indexed: 05/21/2023]
Abstract
Discriminative base motifs within DNA templates for fluorescent silver clusters are identified using methods that combine large experimental data sets with machine learning tools for pattern recognition. Combining the discovery of certain multibase motifs important for determining fluorescence brightness with a generative algorithm, the probability of selecting DNA templates that stabilize fluorescent silver clusters is increased by a factor of >3.
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Affiliation(s)
- Stacy M Copp
- Physics Department, UCSB, Santa Barbara, CA, 93106, USA
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35
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Pu F, Ren J, Qu X. Nucleic acids and smart materials: advanced building blocks for logic systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:5742-57. [PMID: 25042025 DOI: 10.1002/adma.201401617] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 05/11/2023]
Abstract
Logic gates can convert input signals into a defined output signal, which is the fundamental basis of computing. Inspired by molecular switching from one state to another under an external stimulus, molecular logic gates are explored extensively and recognized as an alternative to traditional silicon-based computing. Among various building blocks of molecular logic gates, nucleic acid attracts special attention owing to its specific recognition abilities and structural features. Functional materials with unique physical and chemical properties offer significant advantages and are used in many fields. The integration of nucleic acids and functional materials is expected to bring about several new phenomena. In this Progress Report, recent progress in the construction of logic gates by combining the properties of a range of smart materials with nucleic acids is introduced. According to the structural characteristics and composition, functional materials are categorized into three classes: polymers, noble-metal nanomaterials, and inorganic nanomaterials. Furthermore, the unsolved problems and future challenges in the construction of logic gates are discussed. It is hoped that broader interests in introducing new smart materials into the field are inspired and tangible applications for these constructs are found.
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Affiliation(s)
- Fang Pu
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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Nikitin MP, Shipunova VO, Deyev SM, Nikitin PI. Biocomputing based on particle disassembly. NATURE NANOTECHNOLOGY 2014; 9:716-722. [PMID: 25129073 DOI: 10.1038/nnano.2014.156] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Nanoparticles with biocomputing capabilities could potentially be used to create sophisticated robotic devices with a variety of biomedical applications, including intelligent sensors and theranostic agents. DNA/RNA-based computing techniques have already been developed that can offer a complete set of Boolean logic functions and have been used, for example, to analyse cells and deliver molecular payloads. However, the computing potential of particle-based systems remains relatively unexplored. Here, we show that almost any type of nanoparticle or microparticle can be transformed into autonomous biocomputing structures that are capable of implementing a functionally complete set of Boolean logic gates (YES, NOT, AND and OR) and binding to a target as result of a computation. The logic-gating functionality is incorporated into self-assembled particle/biomolecule interfaces (demonstrated here with proteins) and the logic gating is achieved through input-induced disassembly of the structures. To illustrate the capabilities of the approach, we show that the structures can be used for logic-gated cell targeting and advanced immunoassays.
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Affiliation(s)
- Maxim P Nikitin
- 1] Prokhorov General Physics Institute, Russian Academy of Sciences, Natural Science Centre, 38 Vavilov St, Moscow 119991, Russia [2] Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, Moscow 117997, Russia [3] Moscow Institute of Physics and Technology, 9 Institutskii per., Dolgoprudny, Moscow Region 141700, Russia
| | - Victoria O Shipunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, Moscow 117997, Russia
| | - Sergey M Deyev
- 1] Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, Moscow 117997, Russia [2] Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Av., Nizhny Novgorod 603950, Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute, Russian Academy of Sciences, Natural Science Centre, 38 Vavilov St, Moscow 119991, Russia
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Jiang XJ, Ng DKP. Sequential logic operations with a molecular keypad lock with four inputs and dual fluorescence outputs. Angew Chem Int Ed Engl 2014; 53:10481-4. [PMID: 25078949 DOI: 10.1002/anie.201406002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Indexed: 12/19/2022]
Abstract
A novel coumarin-rhodamine conjugate was prepared, and its metal binding properties were studied by UV/Vis and fluorescence spectroscopy. The conjugate serves as a ratiometric and highly selective fluorescent sensor for Hg(2+) ions. Its metal-responsive spectral properties were utilized to construct a molecular keypad lock with four inputs and dual fluorescence outputs. The complexity of this molecular logic network can greatly enhance the security level of this device.
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Affiliation(s)
- Xiong-Jie Jiang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China)
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Jiang XJ, Ng DKP. Sequential Logic Operations with a Molecular Keypad Lock with Four Inputs and Dual Fluorescence Outputs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Huang Z, Wang H, Yang W. Glutathione-facilitated design and fabrication of gold nanoparticle-based logic gates and keypad lock. NANOSCALE 2014; 6:8300-8305. [PMID: 24933044 DOI: 10.1039/c4nr01615g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper, we describe how we developed a simple design and fabrication method for logic gates and a device by using a commercially available tripeptide, namely glutathione (GSH), together with metal ions and disodium ethylenediaminetetraacetate (EDTA) to control the dispersion and aggregation of gold nanoparticles (NPs). With the fast adsorption of GSH on gold NPs and the strong coordination of GSH with metal ions, the addition of GSH and Pb(2+) ions immediately resulted in the aggregation of gold NPs, giving rise to an AND function. Either Pb(2+) or Ba(2+) ions induced the aggregation of gold NPs in the presence of GSH, supporting an OR gate. Based on the fact that EDTA has a strong capacity to bind metal ions, thus preventing the aggregation of gold NPs, an INHIBIT gate was also fabricated. More interestingly, we found that the addition sequence of GSH and Hg(2+) ions influenced the aggregation of gold NPs in a controlled manner, which was used to design a sequential logic gate and a three-input keypad lock for potential use in information security. The GSH strategy addresses concerns of low cost, simple fabrication, versatile design and easy operation, and offers a promising platform for the development of functional logic systems.
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Affiliation(s)
- Zhenzhen Huang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P.R. China.
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Ran X, Pu F, Ren J, Qu X. DNA-regulated upconverting nanoparticle signal transducers for multivalued logic operation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:1500-1503. [PMID: 24482359 DOI: 10.1002/smll.201303138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/26/2013] [Indexed: 06/03/2023]
Affiliation(s)
- Xiang Ran
- State Key Laboratory of Rare Earth Resource, Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun, 130022, China; Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, 130022, China
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Lin B, Sun Q, Liu K, Lu D, Fu Y, Xu Z, Zhang W. Label-free colorimetric protein assay and logic gates design based on the self-assembly of hemin-graphene hybrid nanosheet. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:2144-2151. [PMID: 24559089 DOI: 10.1021/la4048769] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Here we report a label-free colorimetric method for protein assay based on the intrinsic peroxidase-like catalytic activity of DNA-hemin-graphene (DNA-GH) composite. By using aptamers as protein recognition elements, protein-mediated aggregation of the DNA-GH composite leads to the decrease or increase of the colorimetric signal depending on the sandwich or competitive design strategy. Thrombin and PDGF-BB were chosen as model analytes and the detection limits (LOD) by this method were estimated to be 0.5 nM and 5 nM, respectively. Compared to traditional ELISA method for protein detection, this method possesses the advantages of high sensitivity, simplicity, and low cost. In addition, by designing different DNA-modified hemin-graphene (GH) constructs, using proteins as inputs, the "OR" and "INHIBIT" logic gates were built. This procedure does not require chemical modification on the aptamer probes or analytes and circumvents the limitation associated with the number of target binding sites. Given the attractive analytical characteristics and distinct advantages of DNA-GH composite, the universal approach can be widely applied for the detection of diverse proteins and for the design of versatile logic gates.
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Affiliation(s)
- Bin Lin
- Department of Chemistry, East China Normal University , Shanghai 200062, People's Republic of China
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Pu F, Ju E, Ren J, Qu X. Multiconfigurable logic gates based on fluorescence switching in adaptive coordination polymer nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1111-1117. [PMID: 24243760 DOI: 10.1002/adma.201304109] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/06/2013] [Indexed: 06/02/2023]
Abstract
Fluorescence switching of guest molecules confined in coordination polymer nanoparticles (CPNs) generated from nucleotides and lanthanide ions are used to construct multiconfigurable logic gates. Moreover, the potential of the material as fluorescent probe with large Stokes shift is demonstrated for cellular imaging. In this work the logic gate is integrated into the therapeutic agent and this will be highly beneficial in future molecular computing.
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Affiliation(s)
- Fang Pu
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, (P. R. China)
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Gui R, Jin H, Liu X, Wang Z, Zhang F, Xia J, Yang M, Bi S. Retracted Article: Upconversion luminescent logic gates and turn-on sensing of glutathione based on two-photon excited quantum dots conjugated with dopamine. Chem Commun (Camb) 2014; 50:14847-50. [DOI: 10.1039/c4cc06181k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This article reported the two-photon excited quantum dots-based novel upconversion luminescent logic gates for turn-on sensing of glutathione.
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Affiliation(s)
- Rijun Gui
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
| | - Hui Jin
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
| | - Xifeng Liu
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- P. R. China
| | - Zonghua Wang
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
| | - Feifei Zhang
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
| | - Jianfei Xia
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
| | - Min Yang
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
| | - Sai Bi
- Laboratory of Fiber Materials and Modern Textiles, the Growing Base for State Key Laboratory
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials
- College of Chemical Science and Engineering
- Qingdao University
- Qingdao
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Choi H, Lee JH, Jung JH. Fluorometric/colorimetric logic gates based on BODIPY-functionalized mesoporous silica. Analyst 2014; 139:3866-70. [DOI: 10.1039/c4an00251b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We have demonstrated that metal ions acting as modulators in BODIPY-functionalized SiO2 nanoparticles can generate absorbance changes in accordance with the operation of a half-adder digital circuit.
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Affiliation(s)
- Heekyoung Choi
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University
- Jinju, Korea
| | - Ji Ha Lee
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University
- Jinju, Korea
| | - Jong Hwa Jung
- Department of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University
- Jinju, Korea
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Schultz D, Copp SM, Markešević N, Gardner K, Oemrawsingh SSR, Bouwmeester D, Gwinn E. Dual-color nanoscale assemblies of structurally stable, few-atom silver clusters, as reported by fluorescence resonance energy transfer. ACS NANO 2013; 7:9798-807. [PMID: 24090435 DOI: 10.1021/nn4033097] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We develop approaches to hold fluorescent silver clusters composed of only 10-20 atoms in nanoscale proximity, while retaining the individual structure of each cluster. This is accomplished using DNA clamp assemblies that incorporate a 10 atom silver cluster and a 15 or 16 atom silver cluster. Thermally modulated fluorescence resonance energy transfer (FRET) verifies assembly formation. Comparison to Förster theory, using measured spectral overlaps, indicates that the DNA clamps hold clusters within roughly 5 to 6 nm separations, in the range of the finest resolutions achievable on DNA scaffolds. The absence of spectral shifts in dual-cluster FRET pairs, relative to the individual clusters, shows that select few-atom silver clusters of different sizes are sufficiently stable to retain structural integrity within a single nanoscale DNA construct. The spectral stability of the cluster persists in a FRET pair with an organic dye molecule, in contrast to the blue-shifted emission of the dye.
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Affiliation(s)
- Danielle Schultz
- Chemistry and Biochemistry Department and ‡Physics Department UCSB , Santa Barbara, California 93117, United States
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Rout B, Milko P, Iron MA, Motiei L, Margulies D. Authorizing Multiple Chemical Passwords by a Combinatorial Molecular Keypad Lock. J Am Chem Soc 2013; 135:15330-3. [PMID: 24088016 DOI: 10.1021/ja4081748] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Bhimsen Rout
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Petr Milko
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mark A. Iron
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Leila Motiei
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Margulies
- Departments of †Organic Chemistry and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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He Y, Cui H. Chemiluminescent Logic Gates Based on Functionalized Gold Nanoparticles/Graphene Oxide Nanocomposites. Chemistry 2013; 19:13584-9. [DOI: 10.1002/chem.201301782] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/18/2013] [Indexed: 12/16/2022]
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Li J, Jia X, Li D, Ren J, Han Y, Xia Y, Wang E. Stem-directed growth of highly fluorescent silver nanoclusters for versatile logic devices. NANOSCALE 2013; 5:6131-6138. [PMID: 23728712 DOI: 10.1039/c3nr00998j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This work described for the first time the stem-directed growth of silver nanoclusters (AgNCs) with high brightness using the well-chosen hairpin DNA structure. In comparison with the corresponding double-stranded (ds) DNA capped AgNCs, the fluorescence emission of hairpin DNA structure templated AgNCs were lighted up with 12.5-fold enhancement fluorescent intensity by sequence modification with T-loop. It provided a new prospect for precise placement of nanoscale optical elements onto DNA scaffolds. And these DNA protected AgNCs exhibited the base sequence, strand length and microenvironment-dependent fluorescent properties. Benefiting from these properties, versatile logic gates (or, not, inhibit, XNOR, implication) were constructed using different ions as inputs with AgNCs as signal transducer.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
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Feng L, Zhao A, Ren J, Qu X. Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations. Nucleic Acids Res 2013; 41:7987-96. [PMID: 23814186 PMCID: PMC3763558 DOI: 10.1093/nar/gkt575] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.
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Affiliation(s)
- Lingyan Feng
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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Li M, Yang DP, Wang X, Lu J, Cui D. Mixed protein-templated luminescent metal clusters (Au and Pt) for H2O2 sensing. NANOSCALE RESEARCH LETTERS 2013; 8:182. [PMID: 23601828 PMCID: PMC3643886 DOI: 10.1186/1556-276x-8-182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 04/05/2013] [Indexed: 05/11/2023]
Abstract
A simple and cost-effective method to synthesize the luminescent noble metal clusters (Au and Pt) in chicken egg white aqueous solution at room temperature is reported. The red-emitting Au cluster is used as fluorescent probe for sensitive detection of H2O2.
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Affiliation(s)
- Min Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, 325035, China
- Department of Bio-Nano Science and Engineering, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People’s Republic of China
| | - Da-Peng Yang
- Department of Bio-Nano Science and Engineering, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People’s Republic of China
| | - Xiansong Wang
- Department of Bio-Nano Science and Engineering, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People’s Republic of China
| | - Jianxin Lu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, 325035, China
| | - Daxiang Cui
- Department of Bio-Nano Science and Engineering, Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Institute of Micro-Nano Science and Technology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People’s Republic of China
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