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Yano-Ozawa Y, Lobsiger N, Muto Y, Mori T, Yoshimura K, Yano Y, Stark WJ, Maeda M, Asahi T, Ogawa A, Zako T. Molecular detection using aptamer-modified gold nanoparticles with an immobilized DNA brush for the prevention of non-specific aggregation. RSC Adv 2021; 11:11984-11991. [PMID: 35423740 PMCID: PMC8696536 DOI: 10.1039/d0ra05149g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Gold nanoparticles (AuNPs) are often used for biosensing. In particular, aptamer-modified AuNPs are often used for colorimetric molecular detection, where target molecule-induced AuNP aggregates can be recognized by a color change from red to blue. However, non-specific aggregation could be induced by various compounds, leading to false-positive results. In this work we employed high-density ssDNA modification on the AuNP surface to prevent non-specific aggregation. The covalently immobilized DNA brush was used as an anchor for an aptamer specific for the target molecule. Herein, as a proof-of-concept study, we demonstrated detection of estradiol (E2), one of the endocrine-disrupting estrogen molecules as a model target, in the presence of antibiotic kanamycin (KN) as a model of co-contaminating compounds that induce non-specific aggregation of AuNPs. We also developed a smartphone dark field microscope (DFM) to visualize AuNP aggregation. Our previous study demonstrated that the observation of light scattering by AuNP aggregates with DFM can be applied for versatile molecular detection. In this work, we could successfully detect E2 with the smartphone DFM, and the results were verified by the results from a conventional benchtop DFM. This study would contribute to the future field applicability of AuNP-based sensors. We demonstrated molecular detection using aptamer-modified gold nanoparticles with DNA-brush for the prevention of non-specific aggregation and smartphone darkfield microscopy.![]()
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Affiliation(s)
- Yuki Yano-Ozawa
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Nadine Lobsiger
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan .,Institute for Chemical and Bioengineering, ETH Zürich Wolfgang-Pauli-Strasse 10 CH-8093 Zürich Switzerland
| | - Yu Muto
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan .,Tokyo Research Center, TOSOH Corporation 2743-1 Hayakawa Ayase Kanagawa 252-1123 Japan
| | - Takahiro Mori
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Ken Yoshimura
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Yuki Yano
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Wendelin Jan Stark
- Institute for Chemical and Bioengineering, ETH Zürich Wolfgang-Pauli-Strasse 10 CH-8093 Zürich Switzerland
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Tsuyoshi Asahi
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University 3 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Tamotsu Zako
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
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Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
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Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
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Chang CC, Wang G, Takarada T, Maeda M. Target-Recycling-Amplified Colorimetric Detection of Pollen Allergen Using Non-Cross-Linking Aggregation of DNA-Modified Gold Nanoparticles. ACS Sens 2019; 4:363-369. [PMID: 30628432 DOI: 10.1021/acssensors.8b01156] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Increasing prevalence of pollen allergies has raised concerns about human health. Development of a facile and precise method to detect pollen allergens would thus be of significance for environmental assessments and medical diagnoses. Here we report a sensitive colorimetric method to detect the Japanese cedar pollen allergen, Cry j 2. The method consists of two steps: a signal amplification based on the catalytic DNA hairpin self-assembly, followed by a signal transduction using the salt-induced non-cross-linking aggregation of gold nanoparticles densely modified with short DNA. The assay exhibits a detection limit of 0.2 ng/mL, which is 130-fold greater than that of the previously reported one. Moreover, the assay enables the detection of Cry j 2 spiked in soil solutions by avoiding any interference from the contaminants. The signal amplification system includes an anti-Cry j 2 DNA aptamer, which accounts for the absence of false responses to five nontarget allergen proteins. The present method could be of general applicability to various proteins by using appropriate aptamers.
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Affiliation(s)
- Chia-Chen Chang
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Chutung, Hsinchu 31057, Taiwan
| | - Guoqing Wang
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Ogawa A, Tabuchi J. Biofunction-assisted aptasensors based on ligand-dependent 3' processing of a suppressor tRNA in a wheat germ extract. Org Biomol Chem 2016; 13:6681-5. [PMID: 25962756 DOI: 10.1039/c5ob00794a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a novel type of biofunction-assisted aptasensor that harnesses ligand-dependent 3' processing of a premature amber suppressor tRNA and the subsequent amber suppression of a reporter gene in a wheat germ extract.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
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Zhou Z, Xiao L, Xiang Y, Zhou J, Tong A. A general approach for rational design of fluorescent DNA aptazyme sensors based on target-induced unfolding of DNA hairpins. Anal Chim Acta 2015; 889:179-86. [PMID: 26343441 DOI: 10.1016/j.aca.2015.06.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 01/03/2023]
Abstract
DNA aptazymes are allosteric DNAzymes activated by the targets of DNA aptamers. They take the advantages of both aptamers and DNAzymes, which can recognize specific targets with high selectivity and catalyze multiple-turnover reactions for signal amplification, respectively, and have shown their great promise in many analytical applications. So far, however, the available examples of DNA aptazyme sensors are still limited in utilizing only several DNAzymes and DNA aptamers, most likely due to the lack of a general and simple approach for rational design. Herein, we have developed such a general approach for designing fluorescent DNA aptazyme sensors. In this approach, aptamers and DNAzymes are connected at the ends to avoid any change in their original sequences, therefore enabling the general use of different aptamers and DNAzymes in the design. Upon activation of the aptazymes by the targets of interest, the rate of fluorescence enhancement via the cleavage of a dually labeled substrate by the active aptazymes is then monitored for target quantification. Two DNAzymes and two aptamers are used as examples for the design of three fluorescent aptazyme sensors, and they all show high selectivity and sensitivity for the detection of their targets. More DNA aptazyme sensors for a broader range of targets could be developed by this general approach as long as suitable DNAzymes and aptamers are used.
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Affiliation(s)
- Zhaojuan Zhou
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China; Beijing Third Class Tobacco Supervision Station, Beijing, 101121, China
| | - Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Jun Zhou
- Beijing Third Class Tobacco Supervision Station, Beijing, 101121, China.
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China.
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Carter JR, Balaraman V, Kucharski CA, Fraser TS, Fraser MJ. A novel dengue virus detection method that couples DNAzyme and gold nanoparticle approaches. Virol J 2013; 10:201. [PMID: 23809208 PMCID: PMC3765938 DOI: 10.1186/1743-422x-10-201] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/08/2013] [Indexed: 11/15/2022] Open
Abstract
Background Recent epidemics of dengue viruses (DENV) coupled with new outbreaks on the horizon have renewed the demand for novel detection methods that have the ability to identify this viral pathogen prior to the manifestation of symptoms. The ability to detect DENV in a timely manner is essential for rapid recovery from disease symptoms. A modified lab-derived 10-23 DNAzyme tethered to gold nanoparticles provides a powerful tool for the detection of viruses, such as DENV. Results We examined the effectiveness of coupling DNAzyme (DDZ) activation to the salt-induced aggregation of gold nanoparticles (AuNP) to detect dengue virus (DENV) progeny in mosquito cells. A DNAzyme was designed to recognize the 5’ cyclization sequence (5’ CS) that is conserved among all DENV, and conjugated to AuNPs. DDZ-AuNP has demonstrated the ability to detect the genomic RNA of our model dengue strain, DENV-2 NGC, isolated from infected Aedes albopictus C6/36 cells. These targeting events lead to the rapid aggregation of AuNPs, resulting in a red to clear color transition of the reaction mixes, and thus positive detection of the DENV RNA genome. The inclusion of SDS in the reaction mixture permitted the detection of DENV directly from cell culture supernatants without additional sample processing. Specificity assays demonstrated detection is DENV-specific, while sensitivity assays confirm detection at levels of 1 × 101 TCID50 units. These results demonstrate DDZ-AuNP effectively detects DENV genomes in a sequence specific manner and at concentrations that are practical for field use. Conclusions We have developed an effective detection assay using DNAzyme catalysis coupled with AuNP aggregation for the detection of DENV genomes in a sequence specific manner. Full development of our novel DDZ-AuNP detection method will provide a practical, rapid, and low cost alternative for the detection of DENV in mosquito cells and tissues, and possibly infected patient serum, in a matter of minutes with little to no specialized training required.
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Affiliation(s)
- James R Carter
- Department of Biological Sciences, Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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ZHAO JING, BO BING, YIN YONGMEI, LI GENXI. GOLD NANOPARTICLES-BASED BIOSENSORS FOR BIOMEDICAL APPLICATION. ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1793984412300087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gold nanoparticles are the most extensively studied nanomaterials for biomedical application due to their unique properties, such as rapid and simple synthesis, large surface area, strong adsorption ability and facile conjugation to various biomolecules. The remarkable photophysical properties of gold nanoparticles have provided plenty of opportunities for the preparation of gold nanoparticles-based optical biosensors, while the excellent biocompatibility, conductivity, catalytic properties and large surface-to-volume ratio have facilitated the application of gold nanoparticles in the construction of electrochemical biosensors. In this review, we mainly detail the gold nanoparticles-based optical and electrochemical biosensors for biomedical application in the recent two years, which have exhibited greatly enhanced analytical performances in the detection of DNA, proteins and some important small molecules.
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Affiliation(s)
- JING ZHAO
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - BING BO
- Department of Oncology, The First Affiliated, Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - YONG-MEI YIN
- Department of Oncology, The First Affiliated, Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - GEN-XI LI
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Department of Biochemistry and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P. R. China
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Saha K, Agasti SS, Kim C, Li X, Rotello VM. Gold nanoparticles in chemical and biological sensing. Chem Rev 2012; 112:2739-79. [PMID: 22295941 PMCID: PMC4102386 DOI: 10.1021/cr2001178] [Citation(s) in RCA: 2759] [Impact Index Per Article: 229.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Krishnendu Saha
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Sarit S. Agasti
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Chaekyu Kim
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Xiaoning Li
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
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