1
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Zheng B, Dong H, Zhu J, Zhang Q, Yang S, Yao D. A rational design of a cascaded DNA circuit for nanoparticle assembly and its application in the discrimination of single-base changes. J Mater Chem B 2022; 10:4561-4567. [PMID: 35621087 DOI: 10.1039/d2tb00155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the field of dynamic DNA nanotechnology, a designable DNA assembly circuit based on the toehold-mediated strand displacement reaction has demonstrated its ability to program the self-assembly of nanoparticles. However, the laborious work for the modification of nanoparticles with oligonucleotides, the long assembly time, and the circuit leakage prevent its further and scalable applications. To this end, cascaded circuits composed of two recycling circles are rationally designed in this study. Through the pre-initiation of the autonomous reaction, nanoparticles as sensing elements and no additionally exposed bases on the substrate hybridized with fuel strand, the real assembly time and signal leakage for diagnostic application can be effectively reduced and eliminated, thus offering a promising methodology for future point-of-care testing.
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Affiliation(s)
- Bin Zheng
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Huaze Dong
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Jinmiao Zhu
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Qi Zhang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Shiwei Yang
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei, Anhui 230061, P. R. China.
| | - Dongbao Yao
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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2
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Huang L, Zhang J, Pang L, Hu S, Zhang L, Zhao S. Reversible assembly-disassembly of plasmonic spherical nucleic acids enabling temperature-self-controllable and biomarker-activatable photothermal effects. Chem Commun (Camb) 2021; 57:11617-11620. [PMID: 34643633 DOI: 10.1039/d1cc04792b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the photothermal heating of plasmonic spherical nucleic acids (pSNAs) depends on the self-assembly level and melting temperature (Tm), a temperature-self-controllable and biomarker-activatable photothermal effect in vivo was thus achieved using the Tm-dependent assembly-disassembly of pSNAs.
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Affiliation(s)
- Lixian Huang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China.
| | - Jinling Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China.
| | - Lifang Pang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China.
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China.
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China.
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China.
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3
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Oishi M, Juji S. Acceleration of DNA Hybridization Chain Reactions on 3D Nanointerfaces of Magnetic Particles and Their Direct Application in the Enzyme-Free Amplified Detection of microRNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:35533-35544. [PMID: 34286570 DOI: 10.1021/acsami.1c09631] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accelerated DNA hybridization chain reactions (HCRs) using DNA origami as a scaffold have received considerable attention in dynamic DNA nanotechnology. However, tailor-made designs are essential for DNA origami scaffolds, hampering the practical application of accelerated HCRs. Here, we constructed the semilocalized HCR and localized HCR systems using magnetic beads (MBs) as a simple scaffold to explore them for the enzyme-free miR-21 detection. The semilocalized HCR system relied on free diffusing one hairpin DNA and MBs immobilized with another hairpin DNA, and the localized HCR system relied on MBs coimmobilized with two hairpin DNAs. We demonstrated that the DNA density on MBs plays a critical role in HCR kinetics and limit of detection (LOD). Among semilocalized HCR systems, MBs with a medium DNA density showed a faster HCR and lower LOD (10 pM) than the diffusive (conventional) HCR system (LOD: 86 pM). In contrast, the HCR further accelerated for the localized HCR systems as the DNA density increased. The localized HCR system with the highest DNA density showed the fastest HCR and the lowest LOD (533 fM). These findings are of great importance for the rational design of accelerated HCRs using simple scaffolds for practical applications.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| | - Shotaro Juji
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
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4
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Ghotra G, Le NH, Hayder H, Peng C, Chen JI. Multiplexed and single-cell detection of microRNA with plasmonic nanoparticle assemblies. CAN J CHEM 2021. [DOI: 10.1139/cjc-2021-0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present a label-free, low cost, and miniatured biosensing platform based on the disassembly of core-satellite plasmonic nanoparticle assemblies. The rapid and selective detection of an exemplary nucleic acid biomarker, has-miRNA-210-3p, was achieved via the strand displacement nucleic acid reaction. Target binding leads to dehybridization of the DNA linkers and changes in the scattering properties of nanostructures as monitored by darkfield microscopy. We demonstrate the ability to detect microRNA expunged from single cells and the potential to multiplex discrete assemblies to enable diverse biological applicability. The work may help translate the applicability of microRNA as diagnostic biomarkers, quantitate their abundance in the microenvironment, and facilitate the study of their correlation or causation to other biomolecules at the single-cell level.
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Affiliation(s)
- Gurbrinder Ghotra
- Department of Chemistry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Nguyen H. Le
- Department of Chemistry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Heyam Hayder
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Chun Peng
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Jennifer I.L. Chen
- Department of Chemistry, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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5
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Alladin-Mustan BS, Liu Y, Li Y, de Almeida DRQ, Yuzik J, Mendes CF, Gibbs JM. Reverse transcription lesion-induced DNA amplification: An instrument-free isothermal method to detect RNA. Anal Chim Acta 2021; 1149:238130. [PMID: 33551053 DOI: 10.1016/j.aca.2020.12.005] [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] [Received: 04/24/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022]
Abstract
One challenge in point-of-care (POC) diagnostics is the lack of room-temperature methods for RNA detection based on enzymatic amplification and visualization steps. Here we perform reverse transcription lesion-induced DNA amplification (RT-LIDA), an isothermal amplification method that only requires T4 DNA ligase. RT-LIDA involves the RNA-templated ligation of DNA primers to form complementary DNA (cDNA) followed by toehold-mediated strand displacement of the cDNA and its exponential amplification via our isothermal ligase chain reaction LIDA. Each step is tuned to proceed at 28 °C, which falls within the range of global room temperatures. Using RT-LIDA, we can detect as little as ∼100 amol target RNA and can distinguish RNA target from total cellular RNA. Finally, we demonstrate that the resulting DNA amplicons can be detected colorimetrically, also at room temperature, by rapid, target-triggered disassembly of DNA-modified gold nanoparticles. This integrated amplification/detection platform requires no heating or visualization instrumentation, which is an important step towards realizing instrument-free POC testing.
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Affiliation(s)
| | - Yuning Liu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Yimeng Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Daria R Q de Almeida
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Jesse Yuzik
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Camilla F Mendes
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2.
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6
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Oishi M, Saito K. Simple Single-Legged DNA Walkers at Diffusion-Limited Nanointerfaces of Gold Nanoparticles Driven by a DNA Circuit Mechanism. ACS NANO 2020; 14:3477-3489. [PMID: 32053345 DOI: 10.1021/acsnano.9b09581] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We designed and prepared a single-legged DNA walker that relies on the creation of a simple diffusion-limited nanointerface on a gold nanoparticle (DNA/PEG(+)-GNP) track co-modified with fluorescence-labeled hairpin DNA and poly(ethylene glycol) (PEG) containing a positively charged amino group at one end. The movement of our single-legged DNA walker is driven by an enzyme-free DNA circuit mechanism through cascading toehold mediated DNA displacement reactions (TMDRs) using fuel hairpin DNAs. The acceleration of TMDRs was observed for the DNA/PEG(+)-GNP track through electrostatic interaction between the positively charged track and negatively charged DNAs, resulting in the acceleration of the DNA circuit and amplification of the fluorescence signal. Furthermore, the DNA/PEG(+)-GNP track allowed autonomous and persistent movement of a walker DNA strand on the same GNP track, because the intraparticle DNA circuit occurred preferentially by preventing diffusion of the negatively charged free walker DNA strand from near the positively charged tracks into solution through electrostatic interaction. Based on comparative study of kinetics of TMDRs and DNA walking behaviors, it is to be noted that the DNA/PEG(+)-GNP track showed the fastest DNA circuit reaction (walking rate) and the largest number of steps taken by the walker DNA strand compared to other GNP tracks with varying nanointerfaces that differ in terms of their type of charges (no and negative charges), density of positive charges, and number of hairpin DNAs per GNP track. These facts reveal that the positive charges on the GNP track play an important role in the acceleration of the DNA circuit, as well as the successful walking motion of the single-legged DNA strand. By using the fluorescence signal amplification functions, our single-legged DNA walker could be applied directly and successfully to enzyme-free miRNA-detection systems. The miRNA-detection system provided higher discrimination of other mismatched miRNAs and higher sensitivity (the lowest LOD: 4.0 pM) when compared to other miRNA-detection systems based on other GNP tracks without positive charges. Unlike existing single-legged DNA walkers, our single-legged DNA walkers do not require complex processes, such as immobilization of the walker DNA strand on the tracks and precise adjustment of the sequence of walker DNA. Therefore, our strategy, based on the creation of diffusion-limited nanointerfaces, has enormous potential for the applications of single-legged DNA walkers to biosensors, bioimaging, and computing.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kosuke Saito
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8573, Japan
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7
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Wu Y, Choi N, Chen H, Dang H, Chen L, Choo J. Performance Evaluation of Surface-Enhanced Raman Scattering-Polymerase Chain Reaction Sensors for Future Use in Sensitive Genetic Assays. Anal Chem 2020; 92:2628-2634. [PMID: 31939280 DOI: 10.1021/acs.analchem.9b04522] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a surface-enhanced Raman scattering (SERS)-based polymerase chain reaction (PCR) assay platform for the sensitive and rapid detection of a DNA marker (pagA) of Bacillus anthracis. Real-time quantitative PCR (RT-qPCR) has been recently considered a gold standard for the quantitative evaluation of a target gene, but it still suffers from the problem of a long thermocycling time. To address this issue, we developed a conceptually new SERS-PCR platform and evaluated its performance by sequentially measuring the Raman signals of B. anthracis DNA after the completion of different thermocycling numbers. According to our experimental data, SERS-PCR has lower limits of detection (LODs) than RT-qPCR under the small cycle number of 20. Particularly, it was impossible to detect a target DNA amplicon using RT-qPCR before the number of cycles reached 15, but SERS-PCR enabled DNA detection after only five cycles with an LOD value of 960 pM. In addition, the dynamic range for SERS-PCR (0.1-1000 pM) is wider than that for RT-qPCR (150-1000 pM) under the same condition. We believe that this SERS-PCR technique has a strong potential to be a powerful tool for the rapid and sensitive diagnosis of infectious diseases in the near future.
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Affiliation(s)
- Yixuan Wu
- Department of Chemistry , Chung-Ang University , Seoul 06974 , South Korea
| | - Namhyun Choi
- Department of Bionano Technology , Hanyang University , Ansan 15588 , South Korea
| | - Hao Chen
- Department of Chemistry , Chung-Ang University , Seoul 06974 , South Korea
| | - Hajun Dang
- Department of Chemistry , Chung-Ang University , Seoul 06974 , South Korea
| | - Lingxin Chen
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation , Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003 , China
| | - Jaebum Choo
- Department of Chemistry , Chung-Ang University , Seoul 06974 , South Korea
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8
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Tian Y, Zhang L, Wang L. DNA-Functionalized Plasmonic Nanomaterials for Optical Biosensing. Biotechnol J 2019; 15:e1800741. [PMID: 31464360 DOI: 10.1002/biot.201800741] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/20/2019] [Indexed: 12/15/2022]
Abstract
Plasmonic nanomaterials, especially Au and Ag nanomaterials, have shown attractive physicochemical properties, such as easy functionalization and tunable optical bands. The development of this active subfield paves the way to the fascinating biosensing platforms. In recent years, plasmonic nanomaterials-based sensors have been extensively investigated because they are useful for genetic diseases, biological processes, devices, and cell imaging. In this account, a brief introduction of the development of optical biosensors based on DNA-functionalized plasmonic nanomaterials is presented. Then the common strategies for the application of the optical sensors are summarized, including colorimetry, fluorescence, localized surface plasmon resonance, and surface-enhanced resonance scattering detection. The focus is on the fundamental aspect of detection methods, and then a few examples of each method are highlighted. Finally, the opportunities and challenges for the plasmonic nanomaterials-based biosensing are discussed with the development of modern technologies.
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Affiliation(s)
- Yuanyuan Tian
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China.,Weed Research Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lei Zhang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
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9
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Falahati M, Attar F, Sharifi M, Saboury AA, Salihi A, Aziz FM, Kostova I, Burda C, Priecel P, Lopez-Sanchez JA, Laurent S, Hooshmand N, El-Sayed MA. Gold nanomaterials as key suppliers in biological and chemical sensing, catalysis, and medicine. Biochim Biophys Acta Gen Subj 2019; 1864:129435. [PMID: 31526869 DOI: 10.1016/j.bbagen.2019.129435] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Gold nanoparticles (AuNPs) with unique physicochemical properties have received a great deal of interest in the field of biological, chemical and biomedical implementations. Despite the widespread use of AuNPs in chemical and biological sensing, catalysis, imaging and diagnosis, and more recently in therapy, no comprehensive summary has been provided to explain how AuNPs could aid in developing improved sensing and catalysts systems as well as medical settings. SCOPE OF REVIEW The chemistry of Au-based nanosystems was followed by reviewing different applications of Au nanomaterials in biological and chemical sensing, catalysis, imaging and diagnosis by a number of approaches, and finally synergistic combination therapy of different cancers. Afterwards, the clinical impacts of AuNPs, future application of AuNPs, and opportunities and challenges of AuNPs application were also discussed. MAJOR CONCLUSIONS AuNPs show exclusive colloidal stability and are considered as ideal candidates for colorimetric detection, catalysis, imaging, and photothermal transducers, because their physicochemical properties can be tuned by adjusting their structural dimensions achieved by the different manufacturing methods. GENERAL SIGNIFICANCE This review provides some details about using AuNPs in sensing and catalysis applications as well as promising theranostic nanoplatforms for cancer imaging and diagnosis, and sensitive, non-invasive, and synergistic methods for cancer treatment in an almost comprehensive manner.
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Affiliation(s)
- Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Farnoosh Attar
- Department of Biology, Faculty of Food Industry & Agriculture, Standard Research Institute (SRI), Karaj, Iran
| | - Majid Sharifi
- Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Salihi
- Department of Biology, College of Science, Salahaddin University-Erbil, Kurdistan Region, Iraq; Department of Medical Analysis, Faculty of Science, Tishk International University, Erbil, Iraq
| | - Falah Mohammad Aziz
- Department of Biology, College of Science, Salahaddin University-Erbil, Kurdistan Region, Iraq
| | - Irena Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University, 2 Dunav St., Sofia 1000, Bulgaria
| | - Clemens Burda
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Peter Priecel
- Stephenson Institute for Renewable Energy, Department of Chemistry, University of Liverpool, Crown Street, L69 7ZD Liverpool, United Kingdom
| | - Jose A Lopez-Sanchez
- Stephenson Institute for Renewable Energy, Department of Chemistry, University of Liverpool, Crown Street, L69 7ZD Liverpool, United Kingdom
| | - Sophie Laurent
- General, Organic and Biomedical Chemistry, NMR and Molecular Imaging Laboratory, University of Mons, Avenue Maistriau, 19, B-7000 Mons, Belgium; Center for Microscopy and Molecular Imaging (CMMI), Rue A. Bolland, 8 B-6041 Gosselies, Belgium
| | - Nasrin Hooshmand
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Mostafa A El-Sayed
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
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10
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Zhang L, Zhao C, Zhang Y, Wang L, Wang G, Kanayama N, Takarada T, Maeda M, Liang X. Chemically Fueled Plasmon Switching of Gold Nanorods by Single-Base Pairing of Surface-Grafted DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11710-11716. [PMID: 31407908 DOI: 10.1021/acs.langmuir.9b01537] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interactions between metal ions and biomolecules are crucial to various bioprocesses. Development of plasmon switching nanodevices that exploit these molecular interactions is of fundamental and technological interest. Here, we show plasmon switching based on rapid aggregation/dispersion of double-stranded DNA-modified gold nanorods (dsDNA-AuNRs) that exhibit colloidal behaviors depending on pairing/unpairing of the terminal bases. The dsDNA-AuNRs bearing a thymine-thymine (T-T) mismatch at the penultimate position undergo spontaneous non-cross-linking aggregation in the presence of Hg2+ due to T-Hg-T base pairing. Inversely, the subsequent addition of cysteine (Cys) gives rise to the removal of Hg2+ from the T-Hg-T base pair to reproduce the T-T mismatch, resulting in stable dispersion of the dsDNA-AuNRs. The chemical-responsive plasmon switch allows for the rapid and repeatable cycles at room temperature. The validity of the present method is further exemplified by developing another plasmon switch fueled by Ag+ and Cys by installing the Ag+-binding DNA sequence in the dsDNA-AuNR.
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Affiliation(s)
- Lan Zhang
- College of Food Science and Engineering , Ocean University of China , 5 Yushan Road , Qingdao 266003 , China
| | - Chenlin Zhao
- College of Food Science and Engineering , Ocean University of China , 5 Yushan Road , Qingdao 266003 , China
| | - Yao Zhang
- 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
| | - Guoqing Wang
- College of Food Science and Engineering , Ocean University of China , 5 Yushan Road , Qingdao 266003 , China
- Bioengineering Laboratory , RIKEN Cluster for Pioneering Research , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan
- Laboratory for Marine Drugs and Bioproducts , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
| | - Naoki Kanayama
- Bioengineering Laboratory , RIKEN Cluster for Pioneering Research , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan
- Graduate School of Medicine, Science and Technology , Shinshu University , 4-7-1 Wakasato , Nagano-shi , Nagano 380-8553 , Japan
| | - 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
- Graduate School of Medicine, Science and Technology , Shinshu University , 4-7-1 Wakasato , Nagano-shi , Nagano 380-8553 , Japan
| | - Xingguo Liang
- 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
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11
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Wei B, Yao D, Zheng B, Zhou X, Guo Y, Li X, Li C, Xiao S, Liang H. Facile Strategy for Visible Disassembly of Spherical Nucleic Acids Programmed by Catalytic DNA Circuits. ACS APPLIED MATERIALS & INTERFACES 2019; 11:19724-19733. [PMID: 31083902 DOI: 10.1021/acsami.9b02107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The programmable toehold-mediated DNA-strand-displacement reaction has demonstrated its extraordinary capability in driving the spherical nucleic acid assembly. Here, a facile strategy of integrating a DNA-strand-displacement-based DNA circuit with a universal spherical nucleic acid aggregate system was developed for the visible disassembly of spherical nucleic acids. This integrated system exhibited rapid colorimetric response and good sensitivity in the disassembly reaction and demonstrated its capability in the application of single nucleotide polymorphism discrimination. Moreover, an OR logic gate used for multiplex detection was constructed through combining the fixed spherical nucleic acid disassembly system with two DNA circuits. This strategy will have great potential in the fabrication of a portable low-cost DNA diagnostic kit, and it is also a very promising method to be used in other applications, such as complex DNA networks and programmable phase transformation of nanoparticle superlattices.
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Affiliation(s)
- Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Dongbao Yao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Bin Zheng
- School of Chemistry and Chemical Engineering , Hefei Normal University , Hefei , Anhui 230061 , P. R. China
| | - Xiang Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Yijun Guo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Xiang Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Chengxu Li
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Shiyan Xiao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
| | - Haojun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering , University of Science and Technology of China , Hefei , Anhui 230026 , P. R. China
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12
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Tang Z, Takarada T, Maeda M. Non-Cross-Linking Aggregation of DNA-Carrying Polymer Micelles Triggered by Duplex Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14899-14910. [PMID: 30086233 DOI: 10.1021/acs.langmuir.8b01840] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Colloidal behaviors of particles functionalized with biomolecules are generally complicated. This study describes that colloidal behaviors of double-stranded (ds) DNA-carrying polymer micelles are well controlled by altering the molar ratio of single-stranded (ss) DNA moiety in the dsDNA shell. ssDNA-carrying micelles composed of a poly( N-isopropylacrylamide) (PNIPAAm) core surrounded by a dense shell of ssDNAs were prepared through self-assembly of PNIPAAm grafted with ssDNA by incubating its solution above the lower critical solution temperature. Spontaneous, non-cross-linking aggregation of the micelles was triggered by DNA duplex formation on the surface. Comparison of the critical coagulation concentration of NaCl among a series of the DNA-carrying micelles revealed the relationship between the helical structure of the surface-bound DNA and the colloidal stability of the micelles. The electrophoretic mobility analysis of the micelles indicated that the duplex formation reduced the structural flexibility of the surface-bound DNA, thereby decreasing the interparticle entropic repulsion. It is also suggested that the augmented rigidity of the surface-bound DNA increases the number of terminal base pairs facing the solvent, which could lead to multiple blunt-end stacking interaction among the micelles. Therefore, small DNA molecules could be considered unique surface-modifiers capable of controlling interactions between the surfaces of materials.
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Affiliation(s)
- Zhonglan Tang
- National Engineering Research Center for Biomaterials , Sichuan University , 29 Wangjiang Road , Chengdu 610064 , 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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Huang R, He N, Li Z. Recent progresses in DNA nanostructure-based biosensors for detection of tumor markers. Biosens Bioelectron 2018. [DOI: 10.1016/j.bios.2018.02.053] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Hakimian F, Ghourchian H, Hashemi AS, Arastoo MR, Behnam Rad M. Ultrasensitive optical biosensor for detection of miRNA-155 using positively charged Au nanoparticles. Sci Rep 2018; 8:2943. [PMID: 29440644 PMCID: PMC5811613 DOI: 10.1038/s41598-018-20229-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/11/2018] [Indexed: 01/10/2023] Open
Abstract
An ultrasensitive optical biosensor for microRNA-155 (miR-155) was developed to diagnose breast cancer at early stages. At first, the probe DNA covalently bind to the negatively charged gold nanoparticles (citrate-capped AuNPs). Then, the target miR-155 electrostatically adsorb onto the positively charged gold nanoparticles (polyethylenimine-capped AuNP) surface. Finally, by mixing citrate-capped AuNP/probe and polyethylenimine-capped AuNP/miR-155, hybridization occurs and the optical signal of the mixture give a measure to quantify the miR-155 content. The proposed biosensor is able to specify 3-base-pair mismatches and genomic DNA from target miR-155. The novelty of this biosensor is in its ability to trap the label-free target by its branched positively charged polyethylenimine. This method increases loading the target on the polyethylenimine-capped AuNPs' surface. So, proposed sensor enables miR-155 detection at very low concentrations with the detection limit of 100 aM and a wide linear range from 100 aM to 100 fM.
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Affiliation(s)
- Fatemeh Hakimian
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azam Sadat Hashemi
- Hematology, Oncology & Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Reza Arastoo
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Mohammad Behnam Rad
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Ultrasensitive chemiluminescence assay for the lung cancer biomarker cytokeratin 21-1 via a dual amplification scheme based on the use of encoded gold nanoparticles and a toehold-mediated strand displacement reaction. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2430-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Huang X, Liu Y, Yung B, Xiong Y, Chen X. Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer. ACS NANO 2017; 11:5238-5292. [PMID: 28590117 DOI: 10.1021/acsnano.7b02618] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.
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Affiliation(s)
- Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bryant Yung
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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17
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Shokri E, Hosseini M, Davari MD, Ganjali MR, Peppelenbosch MP, Rezaee F. Disulfide-induced self-assembled targets: A novel strategy for the label free colorimetric detection of DNAs/RNAs via unmodified gold nanoparticles. Sci Rep 2017; 7:45837. [PMID: 28387331 PMCID: PMC5384278 DOI: 10.1038/srep45837] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 12/13/2022] Open
Abstract
A modified non-cross-linking gold-nanoparticles (Au-NPs) aggregation strategy has been developed for the label free colorimetric detection of DNAs/RNAs based on self-assembling target species in the presence of thiolated probes. Two complementary thiol- modified probes, each of which specifically binds at one half of the target introduced SH groups at both ends of dsDNA. Continuous disulfide bond formation at 3' and 5' terminals of targets leads to the self-assembly of dsDNAs into the sulfur- rich and flexible products with different lengths. These products have a high affinity for the surface of Au-NPs and efficiently protect the surface from salt induced aggregation. To evaluate the assay efficacy, a small part of the citrus tristeza virus (CTV) genome was targeted, leading to a detection limit of about 5 × 10-9 mol.L-1 over a linear ranged from 20 × 10-9 to 10 × 10-7 mol.L-1. This approach also exhibits good reproducibility and recovery levels in the presence of plant total RNA or human plasma total circulating RNA extracts. Self-assembled targets can be then sensitively distinguished from non-assembled or mismatched targets after gel electrophoresis. The disulfide reaction method and integrating self-assembled DNAs/RNAs targets with bare AuNPs as a sensitive indicator provide us a powerful and simple visual detection tool for a wide range of applications.
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Affiliation(s)
- Ehsan Shokri
- 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
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, 52056 Aachen, Germany
| | - Mohammad R. 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
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Farhad Rezaee
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Oligonucleotide-based recognition in colloidal systems - opportunities and challenges. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Oishi M, Sugiyama S. An Efficient Particle-Based DNA Circuit System: Catalytic Disassembly of DNA/PEG-Modified Gold Nanoparticle-Magnetic Bead Composites for Colorimetric Detection of miRNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5153-5158. [PMID: 27483209 DOI: 10.1002/smll.201601741] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/27/2016] [Indexed: 05/07/2023]
Abstract
An efficient particle-based DNA circuit system for a new colorimetric miRNA assay is designed and devised based on a catalytic disassembly strategy through a target miRNA-triggered DNA circuit mechanism. The new particle-based DNA circuit system shows a rapid color change as well as significant improvement of sensitivity without need for other enzymes or instruments.
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Affiliation(s)
- Motoi Oishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan.
| | - Satomi Sugiyama
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8573, Japan
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Wang G, Akiyama Y, Shiraishi S, Kanayama N, Takarada T, Maeda M. Cross-Linking versus Non-Cross-Linking Aggregation of Gold Nanoparticles Induced by DNA Hybridization: A Comparison of the Rapidity of Solution Color Change. Bioconjug Chem 2016; 28:270-277. [DOI: 10.1021/acs.bioconjchem.6b00410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqing Wang
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshitsugu Akiyama
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shota Shiraishi
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Kanayama
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tohru Takarada
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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