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Aoki H, Torimura M, Nakazato T. 384-Channel electrochemical sensor array chips based on hybridization-triggered switching for simultaneous oligonucleotide detection. Biosens Bioelectron 2019; 136:76-83. [PMID: 31039490 DOI: 10.1016/j.bios.2019.04.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
We investigated the feasibility of simultaneous detection of multiple environmentally- and biomedically-relevant RNA biomarker target sequences on a single newly fabricated 384-ch sensor array chip aiming at practical application. The individual sensor is composed of a photolithographically-fabricated Au/Cr-based electrode modified with peptide nucleic acid (PNA) probes. The sensor array chips showed sequence-specific responses upon hybridization of the probes with target sequences complementary to the probes in contrast to mismatch versions. The target oligonucleotides have 15-22 mer sequences from messenger RNAs for estrogen-responsive genes and microRNAs for lung cancer biomarkers. The dependence on target concentrations of sensor responses was observed by using a single chip on which experiments for detection of several target concentrations proceeded simultaneously, with the detection limit of 7.33 × 10-8 M. As more realistic samples, oligonucleotide samples amplified by PCR from a synthesized template sequence were applied to the chip. They showed sequence-specific responses, revealing the potential for fabricated sensor array chips to be utilized to analyze PCR samples. Unlike complicated and expensive chips that require nanofabrication, our sensor array chips based on glass coated with gold thin films are simple and can be fabricated from inexpensive and readily available materials.
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Affiliation(s)
- Hiroshi Aoki
- National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Masaki Torimura
- National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tetsuya Nakazato
- National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
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2
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Kurzątkowska K, Sirko A, Zagórski-Ostoja W, Dehaen W, Radecka H, Radecki J. Electrochemical Label-free and Reagentless Genosensor Based on an Ion Barrier Switch-off System for DNA Sequence-Specific Detection of the Avian Influenza Virus. Anal Chem 2015; 87:9702-9. [DOI: 10.1021/acs.analchem.5b01988] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Katarzyna Kurzątkowska
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Agnieszka Sirko
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5A, 02-106 Warsaw, Poland
| | | | - Wim Dehaen
- Department
of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Hanna Radecka
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Jerzy Radecki
- Institute
of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
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3
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Aoki H. Electrochemical Label-Free Nucleotide Sensors. Chem Asian J 2015; 10:2560-73. [PMID: 26227073 DOI: 10.1002/asia.201500449] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/20/2015] [Indexed: 11/10/2022]
Abstract
Numerous researchers have devoted a great deal of effort over the last few decades to the development of electrochemical oligonucleotide detection techniques, owing to their advantages of simple design, inherently small dimensions, and low power requirements. Their simplicity and rapidity of detection makes label-free oligonucleotide sensors of great potential use as first-aid screening tools in the analytical field of environmental measurements and healthcare management. This review article covers label-free oligonucleotide sensors, focusing specifically on topical electrochemical techniques, including intrinsic redox reaction of bases, conductive polymers, the use of electrochemical indicators, and highly ordered probe structures.
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Affiliation(s)
- Hiroshi Aoki
- Environmental Management Research Institute, National Institute of Advanced Industrial, Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
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4
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Yu Y, Wu L, Zhi J. Diamant-Nanodrähte: Herstellung, Struktur, Eigenschaften und Anwendungen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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5
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Yu Y, Wu L, Zhi J. Diamond nanowires: fabrication, structure, properties, and applications. Angew Chem Int Ed Engl 2014; 53:14326-51. [PMID: 25376154 DOI: 10.1002/anie.201310803] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 11/12/2022]
Abstract
C(sp(3) )C-bonded diamond nanowires are wide band gap semiconductors that exhibit a combination of superior properties such as negative electron affinity, chemical inertness, high Young's modulus, the highest hardness, and room-temperature thermal conductivity. The creation of 1D diamond nanowires with their giant surface-to-volume ratio enhancements makes it possible to control and enhance the fundamental properties of diamond. Although theoretical comparisons with carbon nanotubes have shown that diamond nanowires are energetically and mechanically viable structures, reproducibly synthesizing the crystalline diamond nanowires has remained challenging. We present a comprehensive, up-to-date review of diamond nanowires, including a discussion of their synthesis along with their structures, properties, and applications.
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Affiliation(s)
- Yuan Yu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190 (P.R. China)
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Rhoden Smith A, Iverson BL. Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites. J Am Chem Soc 2013; 135:12783-9. [PMID: 23919778 DOI: 10.1021/ja4057344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Zanardi C, Terzi F, Seeber R, Baldoli C, Licandro E, Maiorana S. Peptide nucleic acids tagged with four lysine residues for amperometric genosensors. ARTIFICIAL DNA, PNA & XNA 2012; 3:80-7. [PMID: 22772036 PMCID: PMC3429534 DOI: 10.4161/adna.20777] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A homothymine PNA decamer bearing four lysine residues has been synthesized as a probe for the development of amperometric sensors. On one hand, the four amino groups introduced make this derivative nine times more soluble than the corresponding homothymine PNA decamer and, on the other hand, allow the stable anchoring of this molecule on Au nanostructured surface through the terminal -NH2 moieties. In particular, XPS and electrochemical investigations performed with hexylamine, as a model molecule, indicate that the stable deposition of primary amine derivatives on such a nanostructured surface is possible and involves the free electron doublet on the nitrogen atom. This finding indicates that this PNA derivative is suitable to act as the probe molecule for the development of amperometric sensors.
Thanks to the molecular probe chosen and to the use of a nanostructured surface as the substrate for the sensor assembly, the device proposed makes possible the selective recognition of the target oligonucleotide sequence with very high sensitivity.
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Affiliation(s)
- Chiara Zanardi
- Dipartimento di Chimica, Università degli Studi di Modena e Reggio Emilia, Modena, Italy.
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8
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AOKI H. Development of Novel Gene Detection Methods and Its Application to Rapid Environmental Diagnostic Techniques. BUNSEKI KAGAKU 2012. [DOI: 10.2116/bunsekikagaku.61.763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Hiroshi AOKI
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST)
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Yang N, Zhuang H, Hoffmann R, Smirnov W, Hees J, Jiang X, Nebel CE. Nanocrystalline 3C-SiC Electrode for Biosensing Applications. Anal Chem 2011; 83:5827-30. [DOI: 10.1021/ac201315q] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nianjun Yang
- Fraunhofer Institute for Applied Solid State Physics (IAF), Tullastrasse 72, Freiburg 79108, Germany
| | - Hao Zhuang
- Institute of Materials Engineering, University of Siegen, Paul-Bonatz-Strasse 9-11, Siegen 57076, Germany
| | - René Hoffmann
- Fraunhofer Institute for Applied Solid State Physics (IAF), Tullastrasse 72, Freiburg 79108, Germany
| | - Waldemar Smirnov
- Fraunhofer Institute for Applied Solid State Physics (IAF), Tullastrasse 72, Freiburg 79108, Germany
| | - Jakob Hees
- Fraunhofer Institute for Applied Solid State Physics (IAF), Tullastrasse 72, Freiburg 79108, Germany
| | - Xin Jiang
- Institute of Materials Engineering, University of Siegen, Paul-Bonatz-Strasse 9-11, Siegen 57076, Germany
| | - Christoph E. Nebel
- Fraunhofer Institute for Applied Solid State Physics (IAF), Tullastrasse 72, Freiburg 79108, Germany
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Aoki H, Kitajima A, Tao H. Label-free and ‘signal-on’ DNA detection using a probe DNA terminated with ferrocene and β-cyclodextrin. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.486034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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AOKI H, KITAJIMA A, TAO H. Electrochemical Gene Sensor Arrays Prepared Using Non-contact Nanoliter Array Spotting of Gene Probes. ANAL SCI 2010; 26:367-70. [DOI: 10.2116/analsci.26.367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Hiroshi AOKI
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Akiko KITAJIMA
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hiroaki TAO
- National Institute of Advanced Industrial Science and Technology (AIST)
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12
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Aoki H, Tao H. Signal enhancement for gene detection based on a redox reaction of [Fe(CN)(6)](4-) mediated by ferrocene at the terminal of a peptide nucleic acid as a probe with hybridization-amenable conformational flexibility. ANAL SCI 2008; 24:929-33. [PMID: 18614839 DOI: 10.2116/analsci.24.929] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Electrochemically enhanced DNA detection was demonstrated by utilizing the couple of a synthesized ferrocene-terminated peptide nucleic acid (PNA) with a cysteine anchor and a sacrificial electron donor [Fe(CN)(6)](4-). DNA detection sensors were prepared by modifying a gold electrode surface with a mixed monolayer of the probe PNA and 11-hydroxy-1-undecanethiol (11-HUT), protecting [Fe(CN)(6)](4-) from any unexpected redox reaction. Before hybridization, the terminal ferrocene moiety of the probe was subject to a redox reaction due to the flexible probe structure and, in the presence of [Fe(CN)(6)](4-), the observed current was amplified based on regeneration of the ferrocene moiety. Hybridization decreased the redox current of the ferrocene. This occurred because hybridization rigidified the probe structure: the ferrocene moiety was then removed from the electrode surface, and the redox reaction of [Fe(CN)(6)](4-) was again prevented. The change in the anodic current before and after hybridization was enhanced 1.75-fold by using the electron donor [Fe(CN)(6)](4-). Sequence-specific detection of the complementary target DNA was also demonstrated.
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Affiliation(s)
- Hiroshi Aoki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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Yang N, Uetsuka H, Osawa E, Nebel C. Vertically Aligned Diamond Nanowires for DNA Sensing. Angew Chem Int Ed Engl 2008; 47:5183-5. [DOI: 10.1002/anie.200801706] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Aoki H, Tao H. Label- and marker-free gene detection based on hybridization-induced conformational flexibility changes in a ferrocene-PNA conjugate probe. Analyst 2007; 132:784-91. [PMID: 17646878 DOI: 10.1039/b704214k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a strategy for label-free and marker-free gene detection transducing the hybridization event to an electrochemical signal based on the hybridization-induced conformational flexibility change in probe structure. The probe structure was designed to possess a ferrocene moiety as a reporter part and a cysteine moiety as an anchor part at each end of a peptide nucleic acid (PNA) as a recognition part. Electrochemical examination of probe-modified gold electrodes revealed that the ferrocene moiety was placed at the flexible end of the linear probe chain. Upon hybridization with a complementary target DNA, the resultant rigid duplex restricted the ferrocene motion to the electrode surface, causing a decrease in the observed current. The target DNA was detected with the detection limit of 1.44 x 10(-11) M. Thus the probe functioned as a 'self-reporting probe' and detection of the target DNA was demonstrated without the need for external indicators. Moreover, the sensor electrode was able repeatedly to detect the target DNA by the process of regeneration and could discriminate a mismatched DNA.
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Affiliation(s)
- Hiroshi Aoki
- National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
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16
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Aoki H, Umezawa Y, Vertova A, Rondinini S. Ion-channel Sensors Based on ETH 1001 Ionophore Embedded in Charged-alkanethiol Self-assembled Monolayers on Gold Electrode Surfaces. ANAL SCI 2006; 22:1581-4. [PMID: 17159319 DOI: 10.2116/analsci.22.1581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An ion-channel sensor was demonstrated by immobilizing ETH 1001, an ionophore for ion-selective electrodes, on a gold electrode surface. The approach for preparing the sensor was to incorporate the ionophore into a mixed self-assembled monolayer of 10-mercaptodecanesulfonate and 11-hydroxy-1-undecanethiol formed on the surface. The voltammetric responses for the thus prepared sensor to the primary cation Ca(2+) were observed by using [Fe(CN)(6)](3-/4-) as an electroactive marker. The ionophore was stably immobilized on the electrode surface with the hydrophobic interaction between its alkyl chains and those of the alkanethiol. The introduction of a proper charge density to the electrode surface improved the sensor sensitivity with retaining the selective response to Ca(2+) against Mg(2+) with concentrations above 10(-4) M.
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Affiliation(s)
- Hiroshi Aoki
- Department of Chemistry, School of Science, The University of Tokyo, Japan.
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