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Tang X, Lu M, Wang J, Man S, Peng W, Ma L. Recent Advances of DNA-Templated Metal Nanoclusters for Food Safety Detection: From Synthesis, Applications, Challenges, and Beyond. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5542-5554. [PMID: 38377578 DOI: 10.1021/acs.jafc.3c09621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Food safety concerns have become a significant threat to human health and well-being, catching global attention in recent years. As a result, it is imperative to research conceptually novel biosensing and effective techniques for food matrices detection. Currently, DNA-templated metal nanoclusters (DNA-MNCs) are considered as one of the most promising nanomaterials due to their excellent properties in biosensing. While DNA-MNCs have garnered increasing interest, the reviews of design strategies, applications, and futuristic prospects for biosensing have been hardly found especially in food safety. The synthesis of DNA-MNCs and their use as biosensing materials in food contamination detection, including pathogenic bacteria, toxins, heavy metals, residues of pesticides, and others were comprehensively reviewed. In addition, we summarize the properties of DNA-MNCs briefly and discuss the challenges and future trends. The application of DNA-MNCs powered biosensing has been demonstrated and actively studied, which is a promising paradigm for food safety testing that can supplement or even replace current existing methods. Despite the challenges of difficulty regulating accurately, poor stability, low quantum yield, and difficult commercial transformation, the application prospects of DNA-MNCs biosensors are promising. This review aims to provide insights and directions for the future development of DNA-MNCs based food detection technology.
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Affiliation(s)
- Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiajing Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Weipan Peng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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2
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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3
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Ramasanoff RR, Sokolov PA. Intersystem Crossing Rates of Violet-, Green- and Red-emitting DNA Stabilized Silver Luminescent Clusters. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Lin X, Zou L, Lan W, Liang C, Yin Y, Liang J, Zhou Y, Wang J. Progress of metal nanoclusters in nucleic acid detection. Dalton Trans 2021; 51:27-39. [PMID: 34812463 DOI: 10.1039/d1dt03183j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development and application of metal nanoclusters (MNCs) in nucleic acid testing in the past 10 years have been summarized. Fluorescence enhancement and red shift can occur when the G-rich sequence gets close to Ag NCs or the complementary DNA strand hybridizes with Ag NCs tail strand, which can be used to identify the nucleic acid. Ag NCs with the abasic site in DNA duplex can distinguish mutant genes such as cancer suppression gene p53. Ag NCs with auxiliary DNA can be used to detect miR-21, miR-16-5p, miR-19b-3p, and miR-141. Cu NCs/Cu NPs can recognize miRNA-155, miR-21, and miR-let-7d without auxiliary DNA. Au NCs can identify H1N1 gene fragments by fluorescence quenching caused by proximity to the G-rich sequence. Besides, Au NCs can recognize miRNA-21 and let-7a. SsDNA MNCs adsorbed on the surface of GO and CNPs oxide can be used to identify HBV and HIV gene fragments. The addition of enzymes or auxiliary amplification technologies is a popular way to improve probe sensitivity. Ag NCs combined with TAIEA has the best performance and can obtain LOD as low as aM for miRNA.
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Affiliation(s)
- Xia Lin
- Medical college, Guangxi University, Nanning, 530004, China. .,College of Chemistry and Chemical engineering, Guangxi University, Nanning, 530004, China. .,Guangxi medical college, Nanning, 530023, China.
| | - Lianjia Zou
- Guangxi medical college, Nanning, 530023, China.
| | - Weisen Lan
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | | | - Yanchun Yin
- Guangxi medical college, Nanning, 530023, China.
| | - Jian Liang
- Medical college, Guangxi University, Nanning, 530004, China.
| | | | - Jianyi Wang
- Medical college, Guangxi University, Nanning, 530004, China. .,College of Chemistry and Chemical engineering, Guangxi University, Nanning, 530004, China.
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5
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Fluorescent functional nucleic acid: Principles, properties and applications in bioanalyzing. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Guo Z, Chen Y, Wang Y, Jiang H, Wang X. Advances and challenges in metallic nanomaterial synthesis and antibacterial applications. J Mater Chem B 2021; 8:4764-4777. [PMID: 32207511 DOI: 10.1039/d0tb00099j] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-drug resistant bacterial infection has become one of the most serious threats to global public health. The preparation and application of new antibacterial materials are of great significance for solving the infection problem of bacteria, especially multi-drug resistant bacteria. The exceptional antibacterial effects of metal nanoparticles based on their unique physical and chemical properties make such systems ideal for application as antibacterial drug carriers or self-modified therapeutic agents both in vitro and in vivo. Metal nanoparticles also have admirable clinical application prospects due to their broad antibacterial spectrum, various antibacterial mechanisms and excellent biocompatibility. Nevertheless, the in vivo structural stability, long-term safety and cytotoxicity of the surface modification of metal nanoparticles have yet to be further explored and improved in subsequent studies. Herein, we summarized the research progress concerning the mechanism of metal nanomaterials in terms of antibacterial activity together with the preparation of metal nanostructures. Based on these observations, we also give a brief discussion on the current problems and future developments of metal nanoparticles for antibacterial applications.
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Affiliation(s)
- Zengchao Guo
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yun Chen
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yihan Wang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Hui Jiang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Sadeghan AA, Soltaninejad H, Dadmehr M, Hamidieh AA, Asadollahi MA, Hosseini M, Ganjali MR, Hosseinkhani S. Fluorimetric detection of methylated DNA of Sept9 promoter by silver nanoclusters at intrastrand 6C-loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119081. [PMID: 33128948 DOI: 10.1016/j.saa.2020.119081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Methylation of DNA at carbon 5 of cytosines is the most common epigenetic modification of human genome. Due to its critical role in many normal cell processes such as growth and development, any aberrant methylation pattern in a particular locus may lead to abnormal functions and diseases such as cancer. Development of methods to detect methylation state of DNA which may eliminate labor-intensive chemical or enzymatic treatments has received considerable attention in recent years. Herein, we report a DNA methylation detection procedure based on fluorescence turn-on strategy. Target sequence was selected from Sept9 promoter region that has been reported as one of the most frequently methylated sites in colorectal cancer. Probe DNA was designed to be complementary to this sequence with an additional six cytosines in the middle to form an internal loop to host silver nanoclusters. The fluorescence intensity of the synthesized silver nanoclusters with the duplexes of probe-non-methylated target was significantly different from that of probe-methylated target. The fluorescence enhanced with increasing the methylated DNA concentration with a linear relation in the range of 1.0 × 10-8 M to 5.0 × 10-7 M with the detection limit of 8.2 × 10-9 M, and quenched with non-methylated ones. The method was very specific in the presence of non-complementary sequences with maximum similarity of 40%. Circular dichroism spectra indicated that silver ions significantly affected the structure of methylated and non-methylated DNA into different extents which could further influence the nanocluster fluorescence. Finally, a method was introduced to meet the concerns in the applicability of the proposed method in real situation.
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Affiliation(s)
- Amir Amiri Sadeghan
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Soltaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | | | - Amir Ali Hamidieh
- Pediatric Cell Therapy Research Center, Tehran University of Medical Scienses, Iran
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology & Metabolism Molecular - Cellular Sciences Institute, Iran
| | - Saman Hosseinkhani
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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8
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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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9
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One‐step synthesis of cationic gold nanoclusters with high catalytic activity on luminol chemiluminescence reaction. LUMINESCENCE 2020. [DOI: 10.1002/bio.3916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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10
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Song C, Xu J, Chen Y, Zhang L, Lu Y, Qing Z. DNA-Templated Fluorescent Nanoclusters for Metal Ions Detection. Molecules 2019; 24:E4189. [PMID: 31752270 PMCID: PMC6891495 DOI: 10.3390/molecules24224189] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
DNA-templated fluorescent nanoclusters (NCs) have attracted increasing research interest on account of their prominent features, such as DNA sequence-dependent fluorescence, easy functionalization, wide availability, water solubility, and excellent biocompatibility. Coupling DNA templates with complementary DNA, aptamers, G-quadruplex, and so on has generated a large number of sensors. Additionally, the preparation and applications of DNA-templated fluorescent NCs in these sensing have been widely studied. This review firstly focuses on the properties of DNA-templated fluorescent NCs, and the synthesis of DNA-templated fluorescent NCs with different metals is then discussed. In the third part, we mainly introduce the applications of DNA-templated fluorescent NCs for sensing metal ions. At last, we further discuss the future perspectives of DNA-templated fluorescent NCs in the synthesis and sensing metal ions in the environmental and biological fields.
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Affiliation(s)
- Chunxia Song
- Department of Applied Chemistry, School of Science, Anhui Agricultural University, Hefei 230036, China; (C.S.); (Y.C.); (L.Z.); (Y.L.)
| | - Jingyuan Xu
- Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Ying Chen
- Department of Applied Chemistry, School of Science, Anhui Agricultural University, Hefei 230036, China; (C.S.); (Y.C.); (L.Z.); (Y.L.)
| | - Liangliang Zhang
- Department of Applied Chemistry, School of Science, Anhui Agricultural University, Hefei 230036, China; (C.S.); (Y.C.); (L.Z.); (Y.L.)
| | - Ying Lu
- Department of Applied Chemistry, School of Science, Anhui Agricultural University, Hefei 230036, China; (C.S.); (Y.C.); (L.Z.); (Y.L.)
| | - Zhihe Qing
- Hunan Provincial Engineering Research Center for Food Processing of Aquatic Biotic Resources, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, China;
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11
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Arca-Lafuente S, Martínez-Román P, Mate-Cano I, Madrid R, Briz V. Nanotechnology: A reality for diagnosis of HCV infectious disease. J Infect 2019; 80:8-15. [PMID: 31580870 DOI: 10.1016/j.jinf.2019.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/26/2019] [Indexed: 01/24/2023]
Abstract
Hepatitis C virus (HCV) is the primary etiologic agent of liver cirrhosis or hepatocellular carcinoma. HCV elevated infection rates are mostly due to the lack of an accurate and accessible screening and diagnosis, especially in low- and middle-income countries. Conventional HCV diagnostic algorithm consists of a serological test followed by a nucleic acid test. This sequence of tests is time consuming and not affordable for low-resource settings. Nanotechnology have introduced new promising tests for the diagnose of infectious diseases. Based on the employment of nanoparticles and other nanomaterials which lead to highly sensitive and specific nanoscale tests, most of them target pathogen genome. Implementation of nanoscale tests, which are affordable, portable and easy to use by non-specialized personal, would improve HCV diagnosis algorithm. In this review, we have summed up the current emerging nanotechnology tools, which will improve actual screening and treatment programs, and help to reach HCV elimination proposal.
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Affiliation(s)
- Sonia Arca-Lafuente
- Laboratory of Reference and Research on Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain; BioAssays SL, c/Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Paula Martínez-Román
- Laboratory of Reference and Research on Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Irene Mate-Cano
- Laboratory of Reference and Research on Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Ricardo Madrid
- BioAssays SL, c/Faraday, 7, Parque Científico de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Verónica Briz
- Laboratory of Reference and Research on Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain.
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12
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Borghei YS, Hosseini M, Ganjali MR, Ju H. A unique FRET approach toward detection of single-base mismatch DNA in BRCA1 gene. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 97:406-411. [PMID: 30678926 DOI: 10.1016/j.msec.2018.12.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 10/10/2018] [Accepted: 12/15/2018] [Indexed: 12/17/2022]
Abstract
Early detection of mutation carriers in predisposing genes such as BRCA1 plays an important role in disease prevention. This work developed a quantum dots-based (QDs-based) fluorescence resonance energy transfer (FRET) technique for the detection of single-base mismatch DNA in BRCA1 gene. The FRET between QDs as the donor and silver nanocluster (AgNCs) as the acceptor was designed by the strong interaction between CdTe QDs with appropriate size and dsDNA through binding to its major groove. The dsDNA was formed by the hybridization of ssDNA labeled to AgNCs with target DNA, which introduced CdTe QDs into the major grooves to place the AgNCs in close proximity to the QDs. The complementary and single-base mismatch DNA led to obviously different FRET signals. The FRET signal linearly correlated to the concentration of single-base mismatch DNA in the range of 1.5 × 10-10-1.0 × 10-6 mol L-1. The proposed method showed a detection limit of 80 pmol L-1 and the sensitivity comparable to the previously reported assays, indicating promising potential for single nucleotide polymorphisms diagnosis in clinical application.
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Affiliation(s)
- Yasaman-Sadat Borghei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology & Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210023, China.
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13
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de Carvalho LC, Silveira OJ, Longuinhos R, Nunes RW, Alexandre SS. Optical absorption in complexes of abasic DNA with noble-metal nanoclusters by first principles calculations. Phys Chem Chem Phys 2019; 21:1260-1270. [DOI: 10.1039/c8cp03731k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abasic sites (AP site) in a DNA duplex have been experimentally used to produce fluorescent Ag nanoclusters (NC) with a small number of atoms (n ≤ 6).
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Affiliation(s)
- L. C. de Carvalho
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - O. J. Silveira
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - R. Longuinhos
- Departamento de Física
- Universidade Federal de Lavras
- Caixa Postal 3037
- Lavras
- Brazil
| | - R. W. Nunes
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - S. S. Alexandre
- Departamento de Física
- ICEx
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
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14
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Heinrich F, Riedel M, Lisdat F. Detection of abasic DNA by means of impedance spectroscopy. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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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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16
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Lin F, Zhou Y, Li Q, Zhou X, Shao Y, Habermeyer B, Wang H, Shi X, Xu Z. Prototropically Allosteric Probe for Superbly Selective DNA Analysis. Anal Chem 2017; 89:9299-9306. [DOI: 10.1021/acs.analchem.7b02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Fan Lin
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yufeng Zhou
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qiusha Li
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Institute
of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | | | - Hui Wang
- Chinese
Academy of Sciences (CAS) Key Laboratory of Nanosystem and Hierarchy
Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xinghua Shi
- Chinese
Academy of Sciences (CAS) Key Laboratory of Nanosystem and Hierarchy
Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhiai Xu
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
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17
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Hosseini M, Mohammadi S, Borghei YS, Ganjali MR. Detection of p53 Gene Mutation (Single-Base Mismatch) Using a Fluorescent Silver Nanoclusters. J Fluoresc 2017; 27:1443-1448. [PMID: 28405933 DOI: 10.1007/s10895-017-2083-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 04/04/2017] [Indexed: 02/01/2023]
Abstract
P53 mutation was detected through the application of a biosensing approach based on the decrease in the fluorescence of oligonucleotide-templated silver nanoclusters (DNA-AgNCs). To this end specific DNA scaffolds of two various nucleotide fragments were used. One of the scaffolds was enriched with two cytosine sequence fragment (C12). This led to DNA-AgNCs with a fluorescence intensity through chemical reduction, while the other scaffold acted as the probe fragment (5- GTAGATGGCCATGGCGCGGACGCGGGTG-3). This latter scaffold selectively bound to the specific p53 site. Thus, resulting AgNCs demonstrated decreased fluorescence upon binding to single-base mismatching targets, and this behavior was found to be linearly proportional to the concentration of mutated p53 from 5 to 350 nM and the approach was found to be able to detect concentrations as low as 1.3 nM.
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Affiliation(s)
- Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran. .,Medical Biomaterials Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Shiva Mohammadi
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Yasaman-Sadat Borghei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran.,Biosensor Research Center, Endocrinology & Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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18
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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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19
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Ma JL, Yin BC, Wu X, Ye BC. Copper-Mediated DNA-Scaffolded Silver Nanocluster On–Off Switch for Detection of Pyrophosphate and Alkaline Phosphatase. Anal Chem 2016; 88:9219-25. [DOI: 10.1021/acs.analchem.6b02465] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jin-Liang Ma
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bin-Cheng Yin
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xin Wu
- Department
of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Bang-Ce Ye
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, East China University of Science and Technology, Shanghai, 200237, China
- School
of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, 832000, China
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20
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Longuinhos R, Lúcio AD, Chacham H, Alexandre SS. Charge-transfer optical absorption mechanism of DNA:Ag-nanocluster complexes. Phys Rev E 2016; 93:052413. [PMID: 27300930 DOI: 10.1103/physreve.93.052413] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 06/06/2023]
Abstract
Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:Ag_{4}. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated Ag_{4} or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the Ag_{4} to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-Ag_{4} hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.
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Affiliation(s)
- R Longuinhos
- Departamento de Física, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - A D Lúcio
- Departamento de Física, Universidade Federal de Lavras, Lavras, MG, 37200-000, Brazil
| | - H Chacham
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - S S Alexandre
- Departamento de Física, ICEx, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
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21
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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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22
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Wang Y, Hu Y, Wu T, Zhang L, Liu H, Zhou X, Shao Y. Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 153:645-650. [PMID: 26454091 DOI: 10.1016/j.saa.2015.09.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/26/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect. Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.
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Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Lihua Zhang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Hua Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
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23
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Ma JL, Yin BC, Le HN, Ye BC. Label-Free Detection of Sequence-Specific DNA Based on Fluorescent Silver Nanoclusters-Assisted Surface Plasmon-Enhanced Energy Transfer. ACS APPLIED MATERIALS & INTERFACES 2015; 7:12856-63. [PMID: 26024337 DOI: 10.1021/acsami.5b03837] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have developed a label-free method for sequence-specific DNA detection based on surface plasmon enhanced energy transfer (SPEET) process between fluorescent DNA/AgNC string and gold nanoparticles (AuNPs). DNA/AgNC string, prepared by a single-stranded DNA template encoded two emitter-nucleation sequences at its termini and an oligo spacer in the middle, was rationally designed to produce bright fluorescence emission. The proposed method takes advantage of two strategies. The first one is the difference in binding properties of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) toward AuNPs. The second one is SPEET process between fluorescent DNA/AgNC string and AuNPs, in which fluorescent DNA/AgNC string can be spontaneously adsorbed onto the surface of AuNPs and correspondingly AuNPs serve as "nanoquencher" to quench the fluorescence of DNA/AgNC string. In the presence of target DNA, the sensing probe hybridized with target DNA to form duplex DNA, leading to a salt-induced AuNP aggregation and subsequently weakened SPEET process between fluorescent DNA/AgNC string and AuNPs. A red-to-blue color change of AuNPs and a concomitant fluorescence increase were clearly observed in the sensing system, which had a concentration dependent manner with specific DNA. The proposed method achieved a detection limit of ∼2.5 nM, offering the following merits of simple design, convenient operation, and low experimental cost because of no chemical modification, organic dye, enzymatic reaction, or separation procedure involved.
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Affiliation(s)
| | | | | | - Bang-Ce Ye
- ‡School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, 832000, China
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24
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Ahn JK, Park KS, Won BY, Park HG. A novel electrochemical method to detect theophylline utilizing silver ions captured within abasic site-incorporated duplex DNA. Biosens Bioelectron 2015; 67:590-4. [DOI: 10.1016/j.bios.2014.09.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/20/2014] [Accepted: 09/22/2014] [Indexed: 01/03/2023]
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25
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Cu2+ modulated silver nanoclusters as an on–off–on fluorescence probe for the selective detection of l-histidine. Biosens Bioelectron 2015; 66:103-8. [DOI: 10.1016/j.bios.2014.11.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 11/09/2014] [Indexed: 12/28/2022]
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26
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Gwinn E, Schultz D, Copp SM, Swasey S. DNA-Protected Silver Clusters for Nanophotonics. NANOMATERIALS 2015; 5:180-207. [PMID: 28347005 PMCID: PMC5312861 DOI: 10.3390/nano5010180] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/05/2015] [Indexed: 01/08/2023]
Abstract
DNA-protected silver clusters (AgN-DNA) possess unique fluorescence properties that depend on the specific DNA template that stabilizes the cluster. They exhibit peak emission wavelengths that range across the visible and near-IR spectrum. This wide color palette, combined with low toxicity, high fluorescence quantum yields of some clusters, low synthesis costs, small cluster sizes and compatibility with DNA are enabling many applications that employ AgN-DNA. Here we review what is known about the underlying composition and structure of AgN-DNA, and how these relate to the optical properties of these fascinating, hybrid biomolecule-metal cluster nanomaterials. We place AgN-DNA in the general context of ligand-stabilized metal clusters and compare their properties to those of other noble metal clusters stabilized by small molecule ligands. The methods used to isolate pure AgN-DNA for analysis of composition and for studies of solution and single-emitter optical properties are discussed. We give a brief overview of structurally sensitive chiroptical studies, both theoretical and experimental, and review experiments on bringing silver clusters of distinct size and color into nanoscale DNA assemblies. Progress towards using DNA scaffolds to assemble multi-cluster arrays is also reviewed.
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Affiliation(s)
- Elisabeth Gwinn
- Department of Physics, The University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Danielle Schultz
- Department of Chemistry and Biochemistry, The University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Stacy M Copp
- Department of Physics, The University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Steven Swasey
- Department of Chemistry and Biochemistry, The University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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27
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Zhou Z, Dong S. Protein-DNA interactions: a novel approach to improve the fluorescence stability of DNA/Ag nanoclusters. NANOSCALE 2015; 7:1296-1300. [PMID: 25502467 DOI: 10.1039/c4nr04889j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein-DNA interactions are known to play an important role in a variety of biological processes. We have shown here that protein-DNA binding events can also be used to greatly improve the fluorescence stability of DNA-templated Ag nanoclusters (Ag NCs), which would be highly beneficial for Ag NCs in applications of biosensing/imaging.
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Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.
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28
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Chen J, Chen Q, Gao C, Zhang M, Qin B, Qiu H. A SiO2 NP–DNA/silver nanocluster sandwich structure-enhanced fluorescence polarization biosensor for amplified detection of hepatitis B virus DNA. J Mater Chem B 2015; 3:964-967. [DOI: 10.1039/c4tb01875c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel homogeneous biosensor based on the fluorescence polarization enhancement effect of the SiO2 NP–DNA/Ag nanocluster sandwich structure has been developed for sensitive and selective detection of hepatitis B virus DNA.
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Affiliation(s)
- Jia Chen
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Qiao Chen
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Cunji Gao
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Mingliang Zhang
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Bo Qin
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Hongdeng Qiu
- Key Laboratory of Chemistry of Northwestern Plant Resources
- Key Laboratory for Natural Medicine of Gansu Province
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
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29
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Afonin KA, Schultz D, Jaeger L, Gwinn E, Shapiro BA. Silver nanoclusters for RNA nanotechnology: steps towards visualization and tracking of RNA nanoparticle assemblies. Methods Mol Biol 2015; 1297:59-66. [PMID: 25895995 PMCID: PMC6345514 DOI: 10.1007/978-1-4939-2562-9_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The growing interest in designing functionalized, RNA-based nanoparticles (NPs) for applications such as cancer therapeutics requires simple, efficient assembly assays. Common methods for tracking RNA assemblies such as native polyacrylamide gels and atomic force microscopy are often time-intensive and, therefore, undesirable. Here we describe a technique for rapid analysis of RNA NP assembly stages using the formation of fluorescent silver nanoclusters (Ag NCs). This method exploits the single-stranded specificity and sequence dependence of Ag NC formation to produce unique optical readouts for each stage of RNA NP assembly, obtained readily after synthesis.
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Affiliation(s)
- Kirill A Afonin
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD, 21702, USA
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30
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Nandhini T, Anju KR, Manikandamathavan VM, Vaidyanathan VG, Nair BU. Interactions of Ru(ii) polypyridyl complexes with DNA mismatches and abasic sites. Dalton Trans 2015; 44:9044-51. [DOI: 10.1039/c5dt00807g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ru(ii) polypyridyl complexes bind to CC mismatch DNA with high selectivity.
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Affiliation(s)
- T. Nandhini
- Biophysics Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
- India
| | - K. R. Anju
- Biophysics Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
- India
| | | | - V. G. Vaidyanathan
- Biophysics Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - B. U. Nair
- Chemical Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
- India
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31
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Park KS, Oh SS, Soh HT, Park HG. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline. NANOSCALE 2014; 6:9977-9982. [PMID: 24901073 DOI: 10.1039/c4nr00625a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.
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Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daejeon 305-701, Republic of Korea.
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32
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Peng J, Shao Y, Liu L, Zhang L, Liu H, Wang Y. Ag nanoclusters as probes for turn-on fluorescence recognition of TpG dinucleotide with a high selectivity. Anal Chim Acta 2014; 850:78-84. [PMID: 25441163 DOI: 10.1016/j.aca.2014.08.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/05/2014] [Accepted: 08/14/2014] [Indexed: 01/16/2023]
Abstract
CpG dinucleotide in DNA has a great tendency to mutate to TpG dinucleotide and this transition can cause some serious diseases. In this work, fluorescent Ag nanoclusters (Ag NCs) were employed as useful inorganic fluorophores for the potential of selectively discriminating TpG dinucleotide from CpG dinucleotide. Opposite the base Y of interest in YpG dinucleotide (Y=C or T), a bulge site was introduced so as to make the base Y to be unpaired and ready for Ag(+) binding. Such that the unpaired Y and context base pairs can provide a specific space suitable for creating fluorescent Ag NCs. We found that in comparison with CpG dinucleotide, TpG dinucleotide is much more efficient in growing fluorescent Ag NCs. Therefore, mutation of CpG dinucleotide to TpG can be identified by a turn-on fluorescence response and a high selectivity. More interestingly, Ag NCs exhibit a better performance in the TpG recognition over the other dinucleotides (Y=A and G) than the previously used organic fluorophores. Additionally, the effectiveness of the bulge site design in discriminating these dinucleotides was evidenced by control DNAs having the abasic site structure. We expect that a practical method for TpG dinucleotide recognition with a high selectivity can be developed using the bulge site-grown fluorescent Ag NCs as novel probes.
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Affiliation(s)
- Jian Peng
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, PR China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, PR China.
| | - Lingling Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, PR China
| | - Lihua Zhang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, PR China
| | - Hua Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, PR China
| | - Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, PR China
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33
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Technological applications arising from the interactions of DNA bases with metal ions. Curr Opin Biotechnol 2014; 28:17-24. [DOI: 10.1016/j.copbio.2013.10.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 10/26/2013] [Accepted: 10/31/2013] [Indexed: 01/03/2023]
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34
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Yuan Z, Chen YC, Li HW, Chang HT. Fluorescent silver nanoclusters stabilized by DNA scaffolds. Chem Commun (Camb) 2014; 50:9800-15. [DOI: 10.1039/c4cc02981j] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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36
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Chen J, Zhang X, Cai S, Wu D, Chen M, Wang S, Zhang J. A fluorescent aptasensor based on DNA-scaffolded silver-nanocluster for ochratoxin A detection. Biosens Bioelectron 2014; 57:226-31. [PMID: 24590125 DOI: 10.1016/j.bios.2014.02.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 02/02/2014] [Accepted: 02/05/2014] [Indexed: 02/06/2023]
Abstract
The selective detection of ultratrace amounts of ochratoxin A (OTA) is extremely important for food safety since it is one of the most toxic and widespread mycotoxin. Here we develop a signal-on fluorescent biosensor for detection of OTA based on fluorescent DNA-scaffolded silver-nanocluster (AgNCs), structure-switching of anti-OTA aptamer (Ap) and magnetic beads (MBs), and demonstrate its feasibility in the application of detecting OTA in real samples of wheat. The method exhibits superior sensitivity with a detection limit as low as 2 pg/mL OTA with high specificity. To the best of our knowledge, this is the first attempt to detect OTA based on DNA-scaffolded AgNCs, which possesses relatively high fluorescence quantum yield and photostability with regard to traditional organic dyes and quantum dots. Moreover, combined with the merits of MBs and aptamer, the proposed sensor has many advantages such as fabrication easiness, operation convenience, low cost, and being fast and portable, which may represent a promising path toward routine OTA control.
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Affiliation(s)
- Jinghua Chen
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, China
| | - Xi Zhang
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, China
| | - Shuxian Cai
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, China
| | - Dongzhi Wu
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, China
| | - Mei Chen
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350108, Fujian, China
| | - Shihua Wang
- The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Jing Zhang
- The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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37
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Qing T, Qing Z, Mao Z, He X, Xu F, Wen L, He D, Shi H, Wang K. dsDNA-templated fluorescent copper nanoparticles: poly(AT-TA)-dependent formation. RSC Adv 2014. [DOI: 10.1039/c4ra11551a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Poly(AT-TA) DNA is found to be the specific dsDNA sequence which can act as a highly-efficient template for the formation of dsDNA-templated copper nano-fluorophores.
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Affiliation(s)
- Taiping Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Zhihe Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Zhengui Mao
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Fengzhou Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Li Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Biology
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
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38
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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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39
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40
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Abstract
Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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41
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Schultz D, Gardner K, Oemrawsingh SSR, Markešević N, Olsson K, Debord M, Bouwmeester D, Gwinn E. Evidence for rod-shaped DNA-stabilized silver nanocluster emitters. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2013; 25:2797-803. [PMID: 23371742 DOI: 10.1002/adma.201204624] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/26/2012] [Indexed: 05/10/2023]
Abstract
Fluorescent DNA-stabilized silver nanoclusters contain both cationic and neutral silver atoms. The absorbance spectra of compositionally pure solutions follow the trend expected for rod-shaped silver clusters, consistent with the polarized emission measured from individual nanoclusters. The data suggest a rod-like assembly of silver atoms, with silver cations mediating attachment to the bases.
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Affiliation(s)
- Danielle Schultz
- Chemistry Department, University of California-Santa Barbara, CA 93106, USA
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42
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Obliosca JM, Liu C, Batson RA, Babin MC, Werner JH, Yeh HC. DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters. BIOSENSORS-BASEL 2013; 3:185-200. [PMID: 25586126 PMCID: PMC4263537 DOI: 10.3390/bios3020185] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 12/17/2022]
Abstract
DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and more photostable. Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core. The preparation of DNA/Ag NCs is simple and there is no need to remove excess precursors as these precursors are non-fluorescent. Our recent discovery of the fluorogenic and color switching properties of DNA/Ag NCs have led to the invention of new molecular probes, termed NanoCluster Beacons (NCBs), for DNA detection, with the capability to differentiate single-nucleotide polymorphisms by emission colors. NCBs are inexpensive, easy to prepare, and compatible with commercial DNA synthesizers. Many other groups have also explored and taken advantage of the environment sensitivities of DNA/Ag NCs in creating new tools for DNA/RNA detection and single-nucleotide polymorphism identification. In this review, we summarize the recent trends in the use of DNA/Ag NCs for developing DNA/RNA sensors.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA.
| | - Cong Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA.
| | - Robert Austin Batson
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA.
| | - Mark C Babin
- College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA.
| | - James H Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 78745, USA.
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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43
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Sapsford KE, Algar WR, Berti L, Gemmill KB, Casey BJ, Oh E, Stewart MH, Medintz IL. Functionalizing nanoparticles with biological molecules: developing chemistries that facilitate nanotechnology. Chem Rev 2013; 113:1904-2074. [PMID: 23432378 DOI: 10.1021/cr300143v] [Citation(s) in RCA: 818] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kim E Sapsford
- Division of Biology, Department of Chemistry and Materials Science, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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44
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Abstract
DNA stabilized fluorescent silver nanoclusters are promising materials, of which fluorescent properties can be exploited to develop sensors. Particularly, the presence of a DNA strand in the structure has promoted the development of gene sensors where one part of the sensor is able to recognize the target gene sequence. Moreover, since oligonucleotides can be designed to have binding properties (aptamers) a variety of sensors for proteins and cells have been developed using silver nanoclusters. In this review the applications of this material as sensors of different biomolecules are summarized.
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45
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Ma K, Shao Y, Cui Q, Wu F, Xu S, Liu G. Base-stacking-determined fluorescence emission of DNA abasic site-templated silver nanoclusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15313-15322. [PMID: 22881065 DOI: 10.1021/la301957m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA-templated silver nanoclusters (Ag NCs) are emerging sets of fluorophores that are widely applicable because of high brightness, good photostability, and visible to near-infrared emissions tunable using the DNA sequence and length to change the NC size. We find that fluorescent Ag NCs can be size-selectively grown at DNA abasic sites (AP site) using a constrained duplex environment opposed by a cytosine and flanked by two guanines. The size of the AP site-grown Ag NCs is not affected by the increasing Ag(+) concentration. A Job's plot analysis shows that Ag(2) NCs are the species responsible for the observed emissions. Although varying the DNA sequence one base away from the AP site (i.e., the Ag NC growth site) does not alter the size of the fluorescent Ag NCs, the emissions of the formed Ag NCs are still gradually red shifted as the sequence changes from thymine (T) to cytosine (C), adenine (A), and guanine (G). Furthermore, this emission shift is strongly dependent on the base-stacking direction of the 3'-side sequence of the 5'-G stack exactly flanking the AP site, which exhibits a larger emission alteration than altering the 5'-side sequence of the 3'-G stack flanking the AP site on the other side of the site. The excited-state lifetimes of the Ag NCs are inversely proportional to the singlet energies (ΔE(0,0)) of the Ag NCs relative to their ground state and of the vertical ionization potentials of the guanines directly flanking the AP site as determined by the base stacking. All of these results support the conclusion that the Ag NC excited state becomes more stable by interacting with a guanine base because of the larger electronic dipole moment that can be modified by the stacked sequences. Additionally, the size of the formed Ag NCs seems to be dependent on the consecutive AP site number. Thus, the AP site design in this work provides an easy way to shed light on the role of DNA base stacking in the optical properties of Ag NCs.
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Affiliation(s)
- Kun Ma
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
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46
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Shah P, Rørvig-Lund A, Chaabane SB, Thulstrup PW, Kjaergaard HG, Fron E, Hofkens J, Yang SW, Vosch T. Design aspects of bright red emissive silver nanoclusters/DNA probes for microRNA detection. ACS NANO 2012; 6:8803-14. [PMID: 22947065 DOI: 10.1021/nn302633q] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The influence of the nucleic acid secondary structure on the fast (1 h) formation of bright red emissive silver nanoclusters (AgNCs) in a DNA sequence (DNA-12nt-RED-160), designed for the detection of a microRNA sequence (RNA-miR160), was investigated. The findings show that especially the propensity for mismatch self-dimer formation of the DNA probes can be a good indicator for the creation and stabilization of red emissive AgNCs. Also, the role of the thermal stability of the secondary DNA structures (mismatch self-dimer and hairpin monomers) and the observed AgNC red emission intensity were investigated. These findings can form the basis for a rationale to design new red emissive AgNC-based probes. As an example, a bright red emissive AgNC-based DNA probe was designed for RNA-miR172 detection. The latter opens the possibility to create a variety of AgNC-based DNA probes for the specific detection of plant and animal miRNAs.
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Affiliation(s)
- Pratik Shah
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Copenhagen, Denmark
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47
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Schultz D, Gwinn EG. Silver atom and strand numbers in fluorescent and dark Ag:DNAs. Chem Commun (Camb) 2012; 48:5748-50. [PMID: 22552272 DOI: 10.1039/c2cc17675k] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We use tandem HPLC-mass spectrometry with in-line spectroscopy to identify silver atom numbers, N(Ag), of 10 to 21 in visible- to infrared-emitting Ag:DNA complexes stabilized by oligonucleotide monomers and dimers. Qualitatively different absorbance spectra from bare, same-N(Ag) silver clusters point to silver-base interactions as the origin for the color of Ag:DNAs.
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48
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Latorre A, Somoza Á. DNA-mediated silver nanoclusters: synthesis, properties and applications. Chembiochem 2012; 13:951-8. [PMID: 22508551 DOI: 10.1002/cbic.201200053] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Indexed: 01/19/2023]
Abstract
Fluorescent DNA-AgNCs have emerged as an alternative to standard emitters because of their unique properties: high fluorescent quantum yield, photostability, a broad pallet of colors (blue to near-IR), and the fact that their properties are easily modulated by the DNA sequence and environment. Applications as gene, ion, or small-molecule sensors have been reported.
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49
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Gap site-specific rapid formation of fluorescent silver nanoclusters for label-free DNA nucleobase recognition. Anal Chim Acta 2012; 724:86-91. [PMID: 22483214 DOI: 10.1016/j.aca.2012.02.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 02/16/2012] [Accepted: 02/23/2012] [Indexed: 02/03/2023]
Abstract
Silver nanoclusters (Ag NCs) templated with DNAs have attracted much attention as novel fluorophores because of their convenient emission tunability by the sequence and length of the template DNAs. However, the precise production of Ag NCs in a site-specific manner still remains a challenge to attain highly selective and label-free DNA recognition. Here we exploited the availability of a gap site in DNA duplexes as a new scaffold for the synthesis of Ag NCs. Compared to the commonly used DNA templates for the creation of Ag NCs, the gap site in DNA duplexes was found to facilitate the rapid formation of the fluorescent Ag NCs without sacrifice of their bright emission and excellent stability. We found that fluorescent Ag NCs were highly selectively formed when cytosine faced toward the gap site in DNA duplexes, and they were in situ utilized as readout by signal-on manner for the DNA mutation assays. This base-selective growth of the fluorescent Ag NCs at the gap site would find promising applications in practical detection of single nucleotide polymorphism (SNP) and construction of DNA-based functional sensors with label-free and cost-effective merits.
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50
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Yin J, He X, Wang K, Qing Z, Wu X, Shi H, Yang X. One-step engineering of silver nanoclusters-aptamer assemblies as luminescent labels to target tumor cells. NANOSCALE 2012; 4:110-112. [PMID: 22080331 DOI: 10.1039/c1nr11265a] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We reported one-step engineering of intrinsically fluorescent silver nanoclusters-aptamer assemblies that would allow the development of facile and specific luminescent labels for target tumor cell recognition and analysis.
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Affiliation(s)
- Jinjin Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
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