1
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Enea M, Nuekaew A, Franco R, Pereira E. Gold Nanoprobes for Detection of a Crucial EGFR Deletion for Early Diagnosis of Non-Small-Cell Lung Cancer. BIOSENSORS 2024; 14:162. [PMID: 38667155 PMCID: PMC11048279 DOI: 10.3390/bios14040162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Gold nanoparticles (AuNPs) exhibit improved optical and spectral properties compared to bulk materials, making them suitable for the detection of DNA, RNA, antigens, and antibodies. Here, we describe a simple, selective, and rapid non-cross linking detection assay, using approx. 35 nm spherical Au nanoprobes, for a common mutation occurring in exon 19 of the epidermal growth factor receptor (EGFR), associated with non-small-cell lung cancer cells. AuNPs were synthesized based on the seed-mediated growth method and functionalized with a specific 16 bp thiolated oligonucleotide using a pH-assisted method. Both AuNPs and Au nanoprobes proved to be highly stable and monodisperse through ultraviolet-visible spectrophotometry, dynamic light scattering (DLS), and electrophoretic light scattering (ELS). Our results indicate a detection limit of 1.5 µg mL-1 using a 0.15 nmol dm-3 Au nanoprobe concentration. In conclusion, this work presents an effective possibility for a straightforward, fast, and inexpensive alternative for the detection of DNA sequences related to lung cancer, leading to a potential platform for early diagnosis of lung cancer patients.
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Affiliation(s)
- Maria Enea
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; (A.N.); (E.P.)
| | - Anupong Nuekaew
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; (A.N.); (E.P.)
| | - Ricardo Franco
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Eulália Pereira
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, 687, 4169-007 Porto, Portugal; (A.N.); (E.P.)
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2
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Zhu J, Wang D, Yu H, Yin H, Wang L, Shen G, Geng X, Yang L, Fei Y, Deng Y. Advances in colorimetric aptasensors for heavy metal ion detection utilizing nanomaterials: a comprehensive review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6320-6343. [PMID: 37965993 DOI: 10.1039/d3ay01815f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Heavy metal ion contamination poses significant environmental and health risks, necessitating rapid and efficient detection methods. In the last decade, colorimetric aptasensors have emerged as powerful tools for heavy metal ion detection, owing to their notable attributes such as high specificity, facile synthesis, adaptability to modifications, long-term stability, and heightened sensitivity. This comprehensive overview summarizes the key developments in this field over the past ten years. It discusses the principles, design strategies, and innovative techniques employed in colorimetric aptasensors using nanomaterials. Recent advancements in enhancing sensitivity, selectivity, and on-site applicability are highlighted. The review also presents application studies of successful heavy metal ion detection using colorimetric aptasensors, underlining their potential for environmental monitoring and health protection. Finally, future directions and challenges in the continued evolution of these aptasensors are outlined.
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Affiliation(s)
- Jiangxiong Zhu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Danfeng Wang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
| | - Hong Yu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Hao Yin
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Lumei Wang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Guoqing Shen
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Xueqing Geng
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
| | - Linnan Yang
- School of Big Data, Yunnan Agricultural University, Kunming 650201, China
| | - Yongcheng Fei
- Eryuan County Inspection and Testing Institute, Yunnan 671299, China
| | - Yun Deng
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
- Yunnan Dali Research Institute of Shanghai Jiao Tong University, Yunnan 671000, China
- Eryuan County Inspection and Testing Institute, Yunnan 671299, China
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3
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Hirao G, Fukuzumi N, Ogawa A, Asahi T, Mizuo M, Zako T. Effect of DNA density immobilized on gold nanoparticles on nucleic acid detection. RSC Adv 2023; 13:30690-30695. [PMID: 37869395 PMCID: PMC10585452 DOI: 10.1039/d3ra06528f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors, where target molecule-induced AuNP aggregation can be recognized by a colour change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis due to their rapid and sequence-specific aggregation properties. However, the effect of the density of immobilized ssDNA have not been investigated yet. In this study, we developed a method to control the amount of immobilized ssDNA by use of ethylene glycol, which is expected to control the ice crystal spacing in a freezing-thawing ssDNA-AuNP synthesis method. We also investigated the effect of the DNA density on the sensitivity of the target ssDNA detection, and found that the detection sensitivity was improved at lower DNA densities. To discuss the reason for the improved detection sensitivity, we modified the ssDNA-AuNPs with alkane thiol for better dispersion stability against salt. The results suggest that the DNA density, rather than the dispersion stability, has a significant impact on detection sensitivity.
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Affiliation(s)
- Gen Hirao
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Nanami Fukuzumi
- 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 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Tsuyoshi Asahi
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Maeda Mizuo
- RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 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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4
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He Z, Chen Q, Ding S, Wang G, Takarada T, Maeda M. Suppressed DNA base pair stacking assembly of gold nanoparticles in an alcoholic solvent for enhanced ochratoxin A detection in Baijiu. Analyst 2023; 148:1291-1299. [PMID: 36846974 DOI: 10.1039/d3an00016h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The currently established DNA nanoprobes for the detection of mycotoxin from beverages have been limited by complicated sample pretreatment and uncontrollable nanoparticle flocculation in complex systems. We develop a rapid colorimetric approach for ochratoxin A (OTA) detection in Baijiu in a sample-in/"yes" or "no" answer-out fashion through target-modulated base pair stacking assembly of DNA-functionalized gold nanoparticles (DNA-AuNPs). The colorimetric signification of OTA relies on the competition of OTA with the AuNP surface-grafted DNA in binding with an OTA-targeted aptamer. The specific recognition of OTA by the aptamer prevents DNA duplex formation on the AuNP surface, thereby inhibiting the base pair stacking assembly of the DNA-AuNPs and giving rise to a "turn-on" color. By further suppressing DNA hybridization using a bulged loop design and an alcohol solution, the DNA-AuNPs exhibit an improved reproducibility for OTA sensing while maintaining excellent susceptivity to OTA. A detection limit of 88 nM was achieved along with high specificity towards OTA, which is lower than the maximum tolerated level of OTA in foodstuffs defined by countries worldwide. The entire reaction time, avoiding sample pretreatment, is less than 17 min. The DNA-AuNPs with anti-interference features and sensitive "turn-on" performance promise convenient on-site detection of mycotoxin from daily beverages.
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Affiliation(s)
- Zhiyu He
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Qianyuan Chen
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Shansen Ding
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Tohru Takarada
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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5
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Cheng W, Duan C, Chen Y, Li D, Hou Z, Yao Y, Jiao J, Xiang Y. Highly Sensitive Aptasensor for Detecting Cancerous Exosomes Based on Clover-like Gold Nanoclusters. Anal Chem 2023; 95:3606-3612. [PMID: 36565296 DOI: 10.1021/acs.analchem.2c04280] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Exosome-based liquid biopsy technologies play an increasingly prominent role in tumor diagnosis. However, the simple and sensitive method for counting exosomes still faces considerable challenges. In this work, the CD63 aptamer-modified DNA tetrahedrons on the gold electrode were used as recognition elements for the specific capture of exosomes. Partially complementary DNA probes act as bridges linking trapped exosomes and three AuNP-DNA signal probes. This clover-like structure can tackle the recognition and sensitivity issues arising from the undesired AuNP aggregation event. When cancerous exosomes are present in the system, the high accumulation of methylene blue molecules from DNA-AuNP nanocomposites on the surface of the electrode leads to an intense current signal. According to the results, the aptasensor responds to MCF-7 cell-derived exosomes in the concentration range from 1.0 × 103 to 1.0 × 108 particles·μL-1, with the detection limit of 158 particles·μL-1. Furthermore, the aptasensor has been extended to serum samples from breast cancer patients and exhibited excellent specificity. To sum it up, the aptasensor is sensitive, straightforward, less expensive, and fully capable of receiving widespread application in clinics for tumor monitoring.
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Affiliation(s)
- Wenting Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhiqiang Hou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yanheng Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Jin Jiao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, P. R. China
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6
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Akiyama Y, Kimura K, Komatsu S, Takarada T, Maeda M, Kikuchi A. A Simple Colorimetric Assay of Bleomycin-Mediated DNA Cleavage Utilizing Double-Stranded DNA-Modified Gold Nanoparticles. Chembiochem 2023; 24:e202200451. [PMID: 36156837 PMCID: PMC10092608 DOI: 10.1002/cbic.202200451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/23/2022] [Indexed: 01/05/2023]
Abstract
A colorimetric assay of DNA cleavage by bleomycin (BLM) derivatives was developed utilizing high colloidal stability on double-stranded (ds) DNA-modified gold nanoparticles (dsDNA-AuNPs) possessing a cleavage site. The assay was performed using dsDNA-AuNPs treated with inactive BLM or activated BLM (Fe(II)⋅BLM). A 10-min exposure in dsDNA-AuNPs with inactive BLM treatment resulted in a rapid color change from red to purple because of salt-induced non-crosslinking aggregation of dsDNA-AuNPs. In contrast, the addition of active Fe(II)⋅BLM retained the red color, probably because of the formation of protruding structures at the outermost phase of dsDNA-AuNPs caused by BLM-mediated DNA cleavage. Furthermore, the results of our model experiments indicate that oxidative base release and DNA-cleavage pathways could be visually distinguished with color change. The present methodology was also applicable to model screening assays using several drugs with different mechanisms related to antitumor activity. These results strongly suggest that this assay with a rapid color change could lead to simple and efficient screening of potent antitumor agents.
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Affiliation(s)
- Yoshitsugu Akiyama
- Katsushika Division, Institute of Arts and Sciences, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan.,Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Kazunori Kimura
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Syuuhei Komatsu
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
| | - Tohru Takarada
- Surface and Interface Science Laboratory, RIKEN, 2-1 Hirosawa, 351-0198, Wako, Saitama, Japan
| | - Mizuo Maeda
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, 351-0198, Wako, Saitama, Japan
| | - Akihiko Kikuchi
- Department of Materials Science and Technology, Graduate School of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, 125-8585, Katsushika, Tokyo, Japan
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7
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Colorimetric detection of thrombin based on signal amplification by transcription-reverse transcription concerted reaction using non-crosslinking aggregation of gold nanoparticles. ANAL SCI 2022; 38:3-7. [DOI: 10.1007/s44211-022-00050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 11/01/2022]
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8
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MUTO Y, ZAKO T. Signal-amplified Colorimetric Biosensors Using Gold Nanoparticles. BUNSEKI KAGAKU 2021. [DOI: 10.2116/bunsekikagaku.70.661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yu MUTO
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University
| | - Tamotsu ZAKO
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University
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9
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Cheng L, Wang L, He Z, Sun X, Li Y, Wang G, Tian Y, Takarada T, Maeda M, Liang X. Plasmon switching of gold nanoparticles through thermo-responsive terminal breathing of surface-grafted DNA in hydrated ionic liquids. Analyst 2021; 146:4154-4160. [PMID: 33977966 DOI: 10.1039/d1an00548k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly performed in ionic liquids (ILs) as a unique solvent promises distinct functions and applications in sensors, therapeutics, and optoelectronic devices due to the rich interactions between nanoparticle building blocks and ILs. However, the general consideration that common nanoparticles are readily destabilized by counterions in an IL has largely prevented researchers from investigating controlled nanoparticle assembly in IL-based systems. This study explores the assembling behaviour of double-stranded (ds) DNA-functionalized gold nanoparticles (dsDNA-AuNPs) in hydrated ionic liquids. The DNA base pair stacking assembly of dsDNA-AuNPs occurs at a low IL concentration (<5%). However, a moderate ionic liquid concentration (5-40%) can de-hybridize dsDNA and leaves single-stranded (ss) DNA stabilizing the AuNPs. In concentrated ionic liquids (>40%), interestingly, the higher ionic strength leads to the assembly of DNA-AuNPs. The triphasic assembly trend is also generally observed regardless of the type of IL. By down-regulation of DNA's melting temperature with the IL, the assembly of DNA-AuNPs affords robust response to a lower temperature range, promising applications in plasmonic devices and range-tunable temperature sensors.
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Affiliation(s)
- Lu Cheng
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Luyang Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Zhiyu He
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Xun Sun
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Yujin Li
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China. and Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Yongshuai Tian
- Qingdao Hightop Biotech Co., Ltd, 369 Hedong Road, High-Tech Industrial Development Zone, Qingdao 266111, 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
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China. and Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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10
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Muto Y, Hirao G, Zako T. Transcription-Based Amplified Colorimetric Thrombin Sensor Using Non-Crosslinking Aggregation of DNA-Modified Gold Nanoparticles. SENSORS (BASEL, SWITZERLAND) 2021; 21:4318. [PMID: 34202605 PMCID: PMC8272040 DOI: 10.3390/s21134318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 11/17/2022]
Abstract
Gold nanoparticles (AuNPs) have been employed as colorimetric biosensors due to the color difference between their dispersed (red) and aggregated (blue) states. Although signal amplification reactions triggered by structural changes of the ligands on AuNPs have been widely used to improve measurement sensitivity, the use of ligands is limited. In this study, we designed a AuNP-based signal-amplifying sandwich biosensor, which does not require a conformational change in the ligands. Thrombin was used as a model target, which is recognized by two different probes. In the presence of the target, an extension reaction occurs as a result of hybridization of the two probes. Then RNA synthesis is started by RNA polymerase activation due to RNA promoter duplex formation. The amplified RNA drives aggregation or dispersion of the AuNPs, and a difference of the color if the AuNP solution is observed. As this detection system does not require a conformational change in the ligand, it can be generically applied to a wide range ligands.
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Affiliation(s)
- Yu Muto
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo, Matsuyama 790-8577, Japan; (Y.M.); (G.H.)
- Tokyo Research Center, TOSOH Corporation, 2743-1 Hayakawa, Ayase 252-1123, Japan
| | - Gen Hirao
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo, Matsuyama 790-8577, Japan; (Y.M.); (G.H.)
| | - Tamotsu Zako
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo, Matsuyama 790-8577, Japan; (Y.M.); (G.H.)
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11
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Nakauchi H, Maeda M, Kanayama N. Terminal Sequence-Specific Interparticle Attraction between DNA Duplex-Carrying Polystyrene Microparticles in Aqueous Salt Solution Assessed by Optical Tweezers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5573-5581. [PMID: 33871256 DOI: 10.1021/acs.langmuir.1c00349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The dispersion behavior of DNA duplex-carrying colloidal particles in aqueous high-salt solutions shows extraordinary selectivity against the duplex terminal sequence. We investigated the interparticle force between DNA duplex-carrying polystyrene (dsDNA-PS) microparticles in aqueous salt solutions and examined their behavior in relation to the duplex terminal sequences. Force-distance (F-D) curves for a pair of dsDNA-PS particles were recorded with a dual-beam optical tweezers system with the two optically trapped particles closely approaching each other. Interestingly, only 3-5% of the oligo-DNA strands on the dsDNA-PS particles formed a duplex with complementary DNAs, and the F-D curves showed a distinct specificity to the duplex terminal sequences in the interparticle force at a high-NaCl concentration; a clear attraction peak was observed in F-D curves only when the duplex terminal was a complementary base pair. The attractive strength reached 2.6 ± 0.5 pN at 500 mM NaCl and 4.3 ± 1.0 pN at 750 mM NaCl. By sharp contrast, no significant attraction occurred for the particles with mismatched duplex terminals even at 750 mM NaCl. Similar duplex terminal-specificity in the interparticle force was also confirmed for dsDNA-PS particles in divalent MgCl2 solutions. Considering that the duplex terminal sequences on the dsDNA-PS particles showed only a negligible difference in their surface charges under identical salt conditions, we concluded that the interparticle attraction observed only for the dsDNA-PS particles with complementary duplex terminals is attributable to the salt-facilitated stacking interaction between the paired terminal nucleobases (i.e., blunt-end stacking) on the dsDNA-PS surfaces. Our results thus demonstrate the occurrence of a duplex terminal-specific interparticle force between dsDNA-PS particles under high-salt conditions.
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Affiliation(s)
- Hiroya Nakauchi
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
| | - Mizuo Maeda
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Kanayama
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University, 4-17-1 Wakasato, Nagano-shi, Nagano 380-8553, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Institute of Biomedical Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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12
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Wannapob R, Chuaychob S, Fujita M, Maeda M. Electrochemical Impedimetric Study of Non-Watson-Crick Base Pairs of DNA. ANAL SCI 2021; 37:765-771. [PMID: 33487601 DOI: 10.2116/analsci.20scp21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Electrochemical impedance spectroscopy (EIS) was used to detect non-Watson-Crick base pairs of DNA. Thiol-modified DNA as a probe and mercaptohexanol (MCH) were co-immobilized to form a DNA/MCH mixed self-assembled monolayer on a gold electrode surface and then hybridized with complementary DNAs. The DNA layers were measured by the EIS method and interpreted by equivalent circuits. Every terminal base mismatch of the DNA duplex brought about an increase in the charge-transfer resistance (Rct), unlike the case with a fully matched DNA duplex. The value of Rct was highly sensitive to the number of base mismatches for both unpaired and overhang DNA at the terminal. For internal base mismatches, however, no significant increase in Rct was observed. These experimental results proved that the charge transfer of redox molecules to the electrode surface is largely hindered by an end fraying motion due to base unpairing and dangling overhang. EIS was able to detect these steric properties of DNA strands. Furthermore, an electrode modified with G-quadruplex (G4) DNA demonstrated the influences of bulkiness and loop structure on the accessibility of the redox probe to the electrode.
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Affiliation(s)
| | - Surachada Chuaychob
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Graduate School of Frontier Sciences, The University of Tokyo
| | - Masahiro Fujita
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Graduate School of Frontier Sciences, The University of Tokyo
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13
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Nakauchi H, Maeda M, Kanayama N. DNA Terminal-Specific Dispersion Behavior of Polystyrene Latex Microparticles Densely Covered with Oligo-DNA Strands Under High-Salt Conditions. ANAL SCI 2021; 37:461-468. [PMID: 33281138 DOI: 10.2116/analsci.20scp04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We prepared microspheres densely covered with oligo-DNA strands by immobilizing amino-terminated oligo-DNA strands on the surface of carboxylate polystyrene latex (PS) particles via the amide bond formation. The obtained microspheres (ssDNA-PS) stably dispersed in neutral pH buffer containing high concentrations of NaCl. For the ssDNA-PS ≥1 μm diameter, only 3 - 5% of surface-immobilized oligo-DNA could form a duplex with the complementary strands. Nevertheless, the resulting ssDNA-PS showed a distinct duplex terminal dependency in their dispersion behavior under neutral pH and high NaCl conditions; the microspheres with fully-matched duplexes on the surface spontaneously aggregated in a non-crosslinking manner. By contrast, the microspheres with terminal-mismatched duplexes remained dispersed under the identical conditions. These results suggest that the micrometer-scale particles covered with oligo-DNA strands also have high susceptibility to a duplex terminal sequence in their dispersion property, similar to previously reported DNA-functionalized nanoparticles. This property could potentially be used in various applications including analytical purposes.
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Affiliation(s)
- Hiroya Nakauchi
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University
| | - Mizuo Maeda
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University.,Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Naoki Kanayama
- Department of Biomedical Engineering, Graduate School of Medicine, Science and Technology, Shinshu University.,Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Institute of Biomedical Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
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14
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He Z, Yin H, Chang CC, Wang G, Liang X. Interfacing DNA with Gold Nanoparticles for Heavy Metal Detection. BIOSENSORS 2020; 10:E167. [PMID: 33172098 PMCID: PMC7694790 DOI: 10.3390/bios10110167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
The contamination of heavy metals (e.g., Hg, Pb, Cd and As) poses great risks to the environment and human health. Rapid and simple detection of heavy metals of considerable toxicity in low concentration levels is an important task in biological and environmental analysis. Among the many convenient detection methods for heavy metals, DNA-inspired gold nanoparticles (DNA-AuNPs) have become a well-established approach, in which assembly/disassembly of AuNPs is used for colorimetric signaling of the recognition event between DNA and target heavy metals at the AuNP interface. This review focuses on the recent efforts of employing DNA to manipulate the interfacial properties of AuNPs, as well as the major advances in the colorimetric detection of heavy metals. Beginning with the introduction of the fundamental aspects of DNA and AuNPs, three main strategies of constructing DNA-AuNPs with DNA binding-responsive interface are discussed, namely, crosslinking, electrostatic interaction and base pair stacking. Then, recent achievements in colorimetric biosensing of heavy metals based on manipulation of the interface of DNA-AuNPs are surveyed and compared. Finally, perspectives on challenges and opportunities for future research in this field are provided.
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Affiliation(s)
- Zhiyu He
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
| | - Huiling Yin
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
| | - Chia-Chen Chang
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
- Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan 33302, Taiwan
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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15
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He Z, Wang G, Liang X, Takarada T, Maeda M. DNA Base Pair Stacking Assembly of Anisotropic Nanoparticles for Biosensing and Ordered Assembly. ANAL SCI 2020; 37:415-423. [PMID: 33071270 DOI: 10.2116/analsci.20scr02] [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: 11/23/2022]
Abstract
Anisotropic gold nanoparticles have attracted great interest due to their unique physicochemical properties derived from the shape anisotropy. Manipulation of their interfacial interactions, and thereby the assembling behaviors are often requisite in their applications ranging from optical sensing and diagnosis to self-assembly. Recently, the control of interfacial force based on base pair stacking of DNA terminals have offered a new avenue to surface engineering of nanostructures. In this review, we focus on the DNA base stacking-induced assembly of anisotropic gold nanoparticles, such as nanorods and nanotriangles. The fundamental aspects of anisotropic gold nanoparticles are provided, including the mechanism of the anisotropic growth, the properties arising from the anisotropic shape, and the construction of DNA-grafted anisotropic gold nanoparticles. Then, the advanced applications of their functional assemblies in biosensing and ordered assembly are summarized, followed by a comparison with gold nanospheres. Finally, conclusions and the direction of outlooks are given including future challenges and opportunities in this field.
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Affiliation(s)
- Zhiyu He
- College of Food Science and Engineering, Ocean University of China
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China.,Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao)
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao)
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
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16
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Yang TY, Yu L, Akiyama Y, Takarada T, Maeda M. DNA-Programmed Bimodal 2D Assembly of Differently Sized Nanoparticles via Folding of Precursory Circular Chains. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5588-5595. [PMID: 32378903 DOI: 10.1021/acs.langmuir.0c00765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gold nanoparticle (AuNP) assemblies in two-dimensions (2D) exhibit collective physical/chemical properties that are useful for various devices. However, technical issues still impede the efficient ordering of differently sized AuNPs on solid supports while avoiding phase separation. This paper describes a method to construct binary 2D assemblies by folding precursory circular chains composed of small and large AuNPs. The structural change is caused by a spontaneous, non-cross-linking assembly of fully matched double-stranded DNA-modified AuNPs (dsDNA-AuNPs) at a high ionic strength. Since larger dsDNA-AuNPs have a lower critical coagulation concentration of the supporting electrolyte, the spontaneous assembly of large AuNPs precedes that of small AuNPs in the precursory chain during evaporation. Transmission electron microscopy reveals that alternate-type AuNP chains are folded into a binary 2D structure in a mixed mode, whereas block-type chains are transformed into a binary 2D structure in a core-shell mode. The methodology could potentially be harnessed for the fabrication of binary AuNP arrays for various devices.
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Affiliation(s)
- Tzung-Ying Yang
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8561, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Li Yu
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8561, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Yoshitsugu Akiyama
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
- Faculty of Industrial Science and Technology, Tokyo University of Science, 102-1 Tomino, Oshamambe-cho, Yamakoshi-gun, Hokkaido 049-3514, Japan
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Mizuo Maeda
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8561, Japan
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
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Wang L, Wang G, Shi Y, Zhang L, An R, Takarada T, Maeda M, Liang X. Accelerated non-crosslinking assembly of DNA-functionalized nanoparticles in alcoholic solvents: for application in the identification of clear liquors. Analyst 2020; 145:3229-3235. [PMID: 32191236 DOI: 10.1039/d0an00029a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Colorimetric detection of various target molecules in aqueous solutions based on the non-crosslinking assembly of DNA-functionalized Au nanoparticles (DNA-AuNPs) has been well established in recent years. The extension of DNA-AuNPs to other solvents remains much less explored, despite the practical importance of detection in non-aqueous solutions, such as those containing an organic ingredient that is required or not removable in many contexts. However, the general consideration that DNA is easily denatured and precipitated in organic solvents has been hampering the use of DNA-AuNPs in low polar solvents. Herein, we report a more rapid non-crosslinking assembly of double-stranded (ds) DNA-AuNPs in alcoholic solvents than in aqueous solvents. When the concentration of ethanol in the disperse medium is increased from 0% to 20% (v/v), the rate of non-crosslinking assembly is distinctly increased by a factor of 5-6, whereas the rate is sharply decreased when the ethanol concentration is further increased to 40%. This biphasic kinetics trend could be attributed to the competitive balance between the enhanced intermolecular attraction between dsDNAs and the increased propensity for melting of dsDNA. Rapid naked-eye identification of clear liquors that are encoded by oligonucleotide additives has also been demonstrated by using the alcoholic non-crosslinking assembly of dsDNA-AuNPs as a proof-of-concept.
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Affiliation(s)
- Luyang Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
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