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Hayashi H, Enami A, Fujita H, Kuroiwa S, Ohashi K, Kuwahara M, Osaka T, Momma T. Field-effect transistor biosensor with signal amplification by ternary initiation complexes for detection of wide-range RNA concentration. Talanta 2024; 273:125846. [PMID: 38452594 DOI: 10.1016/j.talanta.2024.125846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/08/2024] [Accepted: 02/28/2024] [Indexed: 03/09/2024]
Abstract
Electrical detection of RNAs using transistor-based biosensors has attracted attention as a strategy for medical diagnosis and environmental monitoring. Herein, we demonstrated a proof-of-concept for specific, sensitive, and label-free RNA detection using a field-effect transistor (FET) biosensor with signal amplification by ternary initiation complexes (SATIC), which is an isothermal one-step nucleic acid amplification initiated by the combination of target RNA, circular DNA template and DNA primer. The SATIC system-applied FET biosensor specifically and quantitatively detected the target RNA with a single-nucleotide difference via the negative charges derived from the amplification products formed by a nucleic acid amplification reaction with φ29 DNA polymerase on the gate surface. In particular, the control of the amplification time allowed the detection of target RNA molecules over a wide concentration range, resulting in a detection limit of up to 6 copies/μL. Therefore, a transistor-based bioassay using the SATIC system could be useful for simple and sensitive nucleic acid analysis.
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Affiliation(s)
- Hiroki Hayashi
- Graduate School of Advanced Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Akihiro Enami
- Graduate School of Advanced Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Hiroto Fujita
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan
| | - Shigeki Kuroiwa
- Research Organization for Nano & Life Innovation, Waseda University, Wasedatsurumaki-cho 513, Shinju-ku, Tokyo, 162-0041, Japan
| | - Keishi Ohashi
- Research Organization for Nano & Life Innovation, Waseda University, Wasedatsurumaki-cho 513, Shinju-ku, Tokyo, 162-0041, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan
| | - Tetsuya Osaka
- Graduate School of Advanced Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Toshiyuki Momma
- Graduate School of Advanced Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo, 169-8555, Japan; Research Organization for Nano & Life Innovation, Waseda University, Wasedatsurumaki-cho 513, Shinju-ku, Tokyo, 162-0041, Japan.
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Lee H, Lee H, Hwang SH, Jeong W, Kim DE. Detection of SARS-CoV-2 RNA through tandem isothermal gene amplification without reverse transcription. Anal Chim Acta 2022; 1212:339909. [PMID: 35623783 PMCID: PMC9073641 DOI: 10.1016/j.aca.2022.339909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
Abstract
Diagnosis of SARS-CoV-2 infection through rapid, accurate, and sensitive testing is the most important and fundamental step in coping with the COVID-19 epidemic. We have developed a sensitive fluorometric assay to detect SARS-CoV-2 viral RNA without thermal cycling. This assay system, based on tandem isothermal gene amplification (TIGA), is composed of ternary rolling circle amplification (t-RCA) and subsequent strand displacement amplification (SDA) coupled with G-quadruplex-generating RCA (SDA/GQ-RCA). Without the need to convert viral RNA into cDNA, viral RNA forms a ternary complex composed of hairpin primer (HP) and dumbbell padlock DNA during the t-RCA process. t-RCA generates a long chain of single-stranded DNA (ssDNA) with tandemly repeated hairpin structures that are subjected to SDA. SDA produces multiple short ssDNAs from t-RCA products, which then serve as primers for the second RCA reaction. A long ssDNA harboring repeated copies of the G-quadruplex is produced in the second round of RCA. Emission of enhanced fluorescence by thioflavin T, which intercalates into the G-quadruplex, allows fluorometric detection of amplified viral genes. This fluorometric analysis sensitively detected SARS-CoV-2 RNA as low as 5.9 aM, with a linear range between 0.2 fM and 200 fM within 1 h. Hence, this isothermal gene amplification method without reverse transcription of viral RNA can be applied to diagnose COVID-19 with high sensitivity and accuracy as an alternative to current PCR-based diagnosis.
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Lee H, Kim DM, Kim DE. Label-free fluorometric detection of influenza viral RNA by strand displacement coupled with rolling circle amplification. Analyst 2021; 145:8002-8007. [PMID: 33410429 DOI: 10.1039/d0an01326a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Since influenza occurs globally every year, it is important to develop a facile and accurate method to detect the influenza virus. This study aimed at developing a sensitive fluorometric assay for detecting influenza viral RNA through tandem gene amplification methods including reverse transcription PCR (RT-PCR), followed by strand displacement amplification (SDA) coupled with rolling circle amplification (RCA). Influenza viral RNA was initially amplified by RT-PCR with a tailed reverse primer containing an additional sequence for SDA. The RT-PCR amplicon was then subjected to SDA, yielding multiple copies of single-stranded DNA (ssDNA) that can be used as a primer for subsequent RCA. Thereafter, a long ssDNA segment harboring tandem repeated G-quadruplexes that were generated through RCA was intercalated by Thioflavin T, yielding a strong fluorescence signal indicating the presence of the target viral RNA. Fluorometric analysis detected influenza viral RNA ranging from 50 pg to 500 pg with a limit of detection of 6.2 pg with a signal-to-background ratio of 10 and identified each influenza virus strain (H1N1, H3N2, and influenza B). Thus, the present method for the label-free fluorometric detection of viral RNA via tandem gene amplifications combining RT-PCR-coupled SDA and G-quadruplex-generating RCA would facilitate the efficient diagnosis of influenza infection.
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Affiliation(s)
- Hyobeen Lee
- Department of Bioscience and Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea.
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Effects of Modifying Thioflavin T at the N3-Position on Its G4 Binding and Fluorescence Emission. Molecules 2020; 25:molecules25214936. [PMID: 33114506 PMCID: PMC7663003 DOI: 10.3390/molecules25214936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
We previously synthesized thioflavin T (ThT) with a hydroxyethyl group introduced at the N3-position (ThT-HE), which binds predominantly to the parallel G-quadruplex (G4) structure found in c-Myc and emits strong fluorescence. In this study, to investigate the effects of introduced substituents on G4 binding and fluorescence emission, a ThT derivative in which the hydroxyl group of ThT-HE was replaced with an amino group (ThT-AE) was synthesized for the first time. Furthermore, three other N3-modified ThT derivatives (ThT-OE2, ThT-SP, and ThT-OE11) having different substituent structures were synthesized by the N-acylation of the terminal amino group of ThT-AE, and their G4-binding and emission properties were investigated. The results showed that, although ThT-AE shows binding selectivity depending on the type of G4, its emission intensity is significantly decreased as compared to that of ThT-HE. However, ThT-OE11, which features an 11-unit oxyethylene chain attached to the terminal amino group of ThT-AE, regained about one-half of the emission intensity of ThT-HE while retaining selectivity for G4s. Accordingly, ThT-OE11 may be used as a key intermediate for synthesizing the conjugates of G4 binders and probes.
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A high affinity modified DNA aptamer containing base-appended bases for human β-defensin. Anal Biochem 2020; 594:113627. [PMID: 32067984 DOI: 10.1016/j.ab.2020.113627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
We used base-appended base modification to develop a new adenine analog, which incorporates an adenine derivative at position 7 of adenine. Using the systematic evolution of ligands by exponential enrichment method with a modified DNA library including this analog, we obtained Aad1, an aptamer that binds strongly to human β-defensin 2, a biomarker of physical stress found in saliva. The dissociation constant of Aad1 with respect to human β-defensin 2 was found to be low (6.8 nM), and was found to bind specifically to human β-defensin 2 in saliva spiked with the protein, as confirmed using pull-down with magnetic beads. To our knowledge, there are no prior reports of nucleic-acid aptamers that bind specifically to human β-defensin 2. However, our results indicated that such adenine analog-containing DNA libraries are extremely effective in the acquisition of high-affinity aptamers.
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Liu J, Feng W, Zhang W. A single-molecule study reveals novel rod-like structures formed by a thrombin aptamer repeat sequence. NANOSCALE 2020; 12:4159-4166. [PMID: 32022812 DOI: 10.1039/c9nr09054a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thrombin aptamers (TBAs) have attracted much attention due to their various applications. The structures and properties of long ssDNA chains with multiple TBA repeat sequences are interesting and distinct from those of their monomers. Due to the complexity of the sample system, it is quite difficult to reveal the structure of such a long-chain ssDNA using traditional methods. In this work, we investigated the repeated ssDNA by using single-molecule magnetic tweezers and AFM imaging. To do that we developed the polymerase change-rolling circle amplification (PC-RCA) synthetic method and prepared two-end modified repeated ssDNA. The rod-like G4 structures formed by intramolecular stacking of the repeat sequence were for the first time identified. This novel structure is different from those higher-order quadruplex structures formed by G-tetrads or loop-mediated interactions. It is also quite interesting to find that the increase of the TBA copy number can unitize the diversity of TBA conformation to the best-fit binding structure for thrombin. The methodology developed in this work can be used for studying other repeat sequences in the genome, such as telomeric DNA as well as interactions of ssDNA with the binding molecule.
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Affiliation(s)
- Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
| | - Wei Feng
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
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Kataoka Y, Fujita H, Afanaseva A, Nagao C, Mizuguchi K, Kasahara Y, Obika S, Kuwahara M. High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives. Biochemistry 2018; 58:493-498. [DOI: 10.1021/acs.biochem.8b01181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuka Kataoka
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Arina Afanaseva
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Chioko Nagao
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
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