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Fan X, Sato Y, Shiraki Y, Nishizawa S. Design of synthetic peptide-based fluorescence probes for turn-on detection of hyaluronan. ANAL SCI 2024; 40:609-614. [PMID: 38214835 PMCID: PMC10961276 DOI: 10.1007/s44211-023-00491-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024]
Abstract
Herein, we designed and examined a series of fluorescent peptide-based probes for turn-on detection of hyaluronan (HA), a member of the glycosaminoglycan family. We utilized two kinds of synthetic HA-binding peptides as the binding unit for HA, and each peptide was coupled with three kinds of environment-sensitive fluorophores as the signaling unit. From the examination of the peptides, fluorophores, and the position and number of fluorophore modification, we found that X7 peptide (RYPISRPRKR) labelled with an aggregation-induced emission (AIE) fluorogen, tetraphenylethene (TPE), at the N-terminal (named TPE-X7) did function as a light-up probe for HA. The response of TPE-X7 was highly selective to higher molecular weight HA in comparison with lower ones, having the possible potential for the analysis of HA size. TPE-X7 was also applicable to the quantification of HA in synovial fluids.
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Affiliation(s)
- Xinyu Fan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.
| | - Yudai Shiraki
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.
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2
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Sekine R, Tsuno S, Irokawa H, Sumitomo K, Han T, Sato Y, Nishizawa S, Takeda K, Kuge S. Inhibition of SARS-CoV-2 nucleocapsid protein-RNA interaction by guanosine oligomeric RNA. J Biochem 2023; 173:447-457. [PMID: 36748338 PMCID: PMC11033527 DOI: 10.1093/jb/mvad008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
The interaction of the β-coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid (N) protein with genomic RNA is initiated by specific RNA regions and subsequently induces the formation of a continuous polymer with characteristic structural units for viral formation. We hypothesized that oligomeric RNAs, whose sequences are absent in the 29.9-kb genome sequence of SARS-CoV-2, might affect RNA-N protein interactions. We identified two such hexameric RNAs, In-1 (CCGGCG) and G6 (GGGGGG), and investigated their effects on the small filamentous/droplet-like structures (< a few μm) of N protein-genomic RNA formed by liquid-liquid phase separation. The small N protein structures were sequence-specifically enhanced by In-1, whereas G6 caused them to coalesce into large droplets. Moreover, we found that a guanosine 12-mer (G12, GGGGGGGGGGGG) expelled preexisting genomic RNA from the small N protein structures. The presence of G12 with the genomic RNA suppressed the formation of the small N protein structures, and alternatively apparently altered phase separation to induce the formation of large droplets with unclear phase boundaries. We showed that the N-terminal RNA-binding domain is required for the stability of the small N protein structures. Our results suggest that G12 may be a strong inhibitor of the RNA-N protein interaction.
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Key Words
- N protein
- RNA Interactions < Protein
- RNA < Viruses
- SARS-CoV-2
- liquid–liquid phase separationAbbreviation: COVID-19, Coronavirus Disease-2019; CTD, C-terminal domain; DIC, differential interference contrast; EMSA, electrophoretic mobility shift assay, IDR, intrinsically disordered region; FITC, fluorescein isothiocyanate; HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, LLPS, liquid–liquid phase separation; NTD, N-terminal domain; N, nucleocapsid; PEG, polyethylene glycol; PNA, peptide nucleic acid; SARS-CoV-2, severe acute respiratory syndrome coronavirus-2; SARS, severe acute respiratory syndrome coronavirus; vRNP, viral ribonucleoprotein
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Affiliation(s)
- Ryoya Sekine
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Satsuki Tsuno
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Hayato Irokawa
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Kazuhiro Sumitomo
- Division of Community Medicine, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi 983-8536, Japan
| | - Tianxue Han
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Azaaoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Azaaoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Azaaoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kouki Takeda
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Shusuke Kuge
- Division of Microbiology, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsuhima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
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3
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Sato Y, Takaku Y, Nakano T, Akamatsu K, Inamura D, Nishizawa S. Synthetic DNA binders for fluorescent sensing of thymine glycol-containing DNA duplexes and inhibition of endonuclease activity. Chem Commun (Camb) 2023; 59:6088-6091. [PMID: 37128964 DOI: 10.1039/d3cc01501g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dimethyllumazine (DML)-thiazole orange (TO) conjugates were developed for fluorescence sensing of thymine glycol (Tg)-containing DNAs based on the selective recognition of the A nucleobase opposite the Tg residue. Additionally, this conjugate has demonstrated an inhibitory activity towards endonuclease III, a DNA repair enzyme, through its competitive binding to Tg-containing DNAs.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yoshihide Takaku
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Toshiaki Nakano
- DNA damage chemistry research group, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Kizugawa, 619-0215, Japan.
| | - Ken Akamatsu
- DNA damage chemistry research group, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Kizugawa, 619-0215, Japan.
| | - Dai Inamura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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4
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Suzuki M, Sato Y, Togashi N, Nishizawa S. Cationic Oligopeptides with Amino Groups as Synthetic Nucleolar Localization Signals for the Rational Design of Nucleolus-Staining Probes. ACS Omega 2023; 8:9592-9596. [PMID: 36936342 PMCID: PMC10018684 DOI: 10.1021/acsomega.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Cationic oligopeptides with amino groups were found to function as synthetic nucleolar localization signals for directing various fluorophores to the nucleolus with high selectivity in the cells with a view toward the development of nucleolus-staining probes.
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5
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Ohira K, Sato Y, Nishizawa S. Self-Assembly and Disassembly of Membrane Curvature-Sensing Peptide-Based Deep-Red Fluorescent Probe for Highly Sensitive Sensing of Exosomes. ACS Sens 2023; 8:522-526. [PMID: 36695520 DOI: 10.1021/acssensors.2c02498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
With increasing knowledge of the diverse roles of exosomes in biological processes, much attention has been paid to the development of analytical methods for exosome analysis. Here, we developed a new class of amphipathic helical (AH) peptide-based fluorescent probes for highly sensitive detection of exosomes in a mix and read manner. Membrane curvature-sensing AH peptide (ApoC) was coupled with lipophilic tail (C12)-carrying thiazole red (TR) for construction of a self-assembly/disassembly based fluorescence "off-on" sensing system for target exosomes. ApoC-TRC12 has extremely weak emission due to the formation of the aggregates, whereas it becomes emissive in response to the target exosomes through the binding-induced disassembly of ApoC-TRC12. We demonstrated that the C12 unit attached to the TR unit had a favorable effect on both fluorescence response (signal-to-background: S/B) and binding affinity. ApoC-TRC12 was applicable to rapid and simple detection of exosomes with high detection sensitivity (limit of detection ≈ 103 particles/μL).
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Affiliation(s)
- Kaito Ohira
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
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6
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He M, Sato Y, Nishizawa S. Classical thiazole orange and its regioisomer as fluorogenic probes for nucleolar RNA imaging in living cells. Analyst 2023; 148:636-642. [PMID: 36602142 DOI: 10.1039/d2an01804g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In contrast to well-established DNA-selective dyes for live cell imaging, RNA-selective dyes have been less developed owing to the challenges of making small molecules have RNA selectivity over DNA. Two kinds of dyes are now commercially available for nucleolar RNA imaging in cells, but these two dyes do not apply to living cells and have limited use in fixed and permeabilized cells. Herein, we report on thiazole orange (TO), a well-known nucleic acid stain, as a promising fluorogenic dye for nucleolar RNA imaging in living cells. TO shows clear response selectivity for RNA over DNA with a significant light-up property upon binding to RNA (λem = 532 nm, I/I0 = 580-fold, and Φbound/Φfree = 380) and is even applicable to wash-free imaging of living cells. More interestingly, 2TO, a regioisomer of TO in which the benzothiazole unit is connected to position 2 in the quinoline ring, performs much better (λem = 532 nm, I/I0 = 430-fold, Φbound/Φfree = 1200), having superior selectivity for RNA in both solution and living cells. The comparison with TO derivatives carrying different substituents at N1 of the quinoline ring reveals that the slight change in the TO framework significantly affects RNA selectivity, photostability and membrane permeability.
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Affiliation(s)
- Mengmeng He
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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7
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Okeke CU, Miura H, Sato Y, Nishizawa S. Kinetic analysis for highly effective triplex formation between small molecule-peptide nucleic acid conjugate probe and Influenza A virus RNA promoter region at neutral pH. Org Biomol Chem 2023; 21:3402-3410. [PMID: 37010004 DOI: 10.1039/d3ob00262d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
In order to overcome pH limitations of triplex-forming peptide nucleic acid (PNA) for the binding to double-stranded RNA (dsRNA), we have recently proposed a new design of triplex-forming PNA-based fluorogenic...
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Affiliation(s)
- Chioma Uche Okeke
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiromasa Miura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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8
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Higuchi K, Sato Y, Togashi N, Suzuki M, Yoshino Y, Nishizawa S. Bright and Light-Up Sensing of Benzo[ c,d]indole-oxazolopyridine Cyanine Dye for RNA and Its Application to Highly Sensitive Imaging of Nucleolar RNA in Living Cells. ACS Omega 2022; 7:23744-23748. [PMID: 35847247 PMCID: PMC9280936 DOI: 10.1021/acsomega.2c02408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Small molecular weight probes that can show a fluorescence signaling response upon binding to RNAs are promising for RNA imaging in living cells. Live-cell RNA imaging probes that can achieve a large light-up ability (>100-fold) and high Φbound value for RNA (>0.50) have been rarely reported to date. Here, benzo[c,d]indole-oxazolopyridine (BIOP), an unsymmetrical monomethine cyanine analogue, was newly developed as a bright and large light-up probe for imaging of nucleolar RNA in living cells. BIOP served as a yellow-emissive probe (λem = 570 nm) and exhibited a significant light-up response upon RNA binding (770-fold) with a high Φbound value (0.52). We demonstrated the advantages of BIOP over a commercially available RNA-staining probe, SYTO RNA select, for robust and sensitive RNA sensing by a systematic comparison of fluorescent properties for RNA. In addition, BIOP was found to possess high membrane permeability and low cytotoxicity in living cells. The examination of live-cell imaging revealed that BIOP exhibited emission in the nucleolus upon binding to nucleolar RNA much stronger than that of SYTO RNA select. Furthermore, BIOP facilitated the highly sensitive imaging of nucleolar RNA, in which 50 nM BIOP can stain nucleolar RNA in living cells with a 20 min incubation.
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9
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Sato Y, Miura H, Tanabe T, Okeke CU, Kikuchi A, Nishizawa S. Fluorescence Sensing of the Panhandle Structure of the Influenza A Virus RNA Promoter by Thiazole Orange Base Surrogate-Carrying Peptide Nucleic Acid Conjugated with Small Molecule. Anal Chem 2022; 94:7814-7822. [PMID: 35604144 DOI: 10.1021/acs.analchem.1c05488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a new class of triplex-forming peptide nucleic acid (PNA)-based fluorogenic probes for sensing of the panhandle structure of the influenza A virus (IAV) RNA promoter region. Here, a small molecule (DPQ) capable of selectively binding to the internal loop structure was conjugated with triplex-forming forced intercalation of the thiazole orange (tFIT) probe with natural PNA nucleobases. The resulting conjugate, tFIT-DPQ, showed a significant light-up response (83-fold) upon strong (Kd = 107 nM) and structure-selective binding to the IAV RNA promoter region under physiological conditions (pH 7.0, 100 mM NaCl). We demonstrated the conjugation of these two units through the suitable spacer was key to show useful binding and fluorogenic signaling functions. tFIT-DPQ facilitated the sensitive and selective detection of IAV RNA based on its binding to the promoter region. Furthermore, we found that tFIT-DPQ could work as a sensitive indicator for screening of test compounds targeting the IAV RNA promoter region in the fluorescence indicator displacement assay.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiromasa Miura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Chioma Uche Okeke
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Akiko Kikuchi
- Department of Kampo and Integrative Medicine, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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10
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Tohgasaki T, Kondo S, Nishizawa S, Ishiwatari S, Sakurai T, Ishikawa S, Takeda A. Evaluation of elastin fibres in young and aged eyelids and abdominal skin using computational 3D structural analysis. Skin Health and Disease 2021; 1:e58. [PMID: 35663779 PMCID: PMC9060010 DOI: 10.1002/ski2.58] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 11/17/2022]
Abstract
Background Aging‐related degeneration of elastic fibres causes skin wrinkles and loss of elasticity. A correlation has been reported between dermal elastic fibre degradation and wrinkles. However, the mechanism of wrinkle formation is complex and unclear. To establish methods for treating wrinkles, it is necessary to understand the aging‐related morphological alterations underlying elastin fibre degradation or disappearance. Objectives To image and analyse aging‐related three‐dimensional (3D) morphological alterations of elastic fibres in the eyelid and abdominal skin. Methods Excised human eyelid and abdominal skin tissues were examined. The structure of elastic fibres in the skin tissues was examined via nuclear, tropoelastin and fibrillin‐1 immunostaining. Then, 3D imaging was performed using a confocal laser microscope and tissue decolourization technology. Images were analysed using a computational method. Results The decolourization technology made it possible to image elastin fibres in 3D, and we devised a method for analyzing the elastin fibre structure using computational methods. It was quantitatively shown that the eyelid skin has a more complex fibrous structure than the abdomen, and the fibres became curved, shortened and thickened with age. Conclusions We provide a novel 3D analysis method for elastin fibres and report age‐related alterations in elastin fibre structure in the human eyelid and abdominal skin. This method contributes to the understanding of elastin fibre degeneration in more detail than conventional methods. Applying this 3D analysis method to skin tissues will contribute to a better understanding of age‐related changes in fibres and to the development of novel wrinkle treatments.
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Affiliation(s)
- T. Tohgasaki
- Fancl Research Institute Fancl Corporation Yokohama Kanagawa Japan
| | - S. Kondo
- Fancl Research Institute Fancl Corporation Yokohama Kanagawa Japan
| | - S. Nishizawa
- Fancl Research Institute Fancl Corporation Yokohama Kanagawa Japan
| | - S. Ishiwatari
- Fancl Research Institute Fancl Corporation Yokohama Kanagawa Japan
| | - T. Sakurai
- Fancl Research Institute Fancl Corporation Yokohama Kanagawa Japan
| | - S. Ishikawa
- Department of Plastic and Aesthetic Surgery Kitasato University School of Medicine Sagamihara Japan
| | - A. Takeda
- Department of Plastic and Aesthetic Surgery Kitasato University School of Medicine Sagamihara Japan
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11
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Sato Y, Igarashi Y, Suzuki M, Higuchi K, Nishizawa S. Deep-red fluorogenic cyanine dyes carrying an amino group-terminated side chain for improved RNA detection and nucleolar RNA imaging. RSC Adv 2021; 11:35436-35439. [PMID: 35493132 PMCID: PMC9042821 DOI: 10.1039/d1ra05872j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/22/2021] [Indexed: 01/01/2023] Open
Abstract
The introduction of an amino-group-terminated side chain into deep-red emissive benzo[c,d]indole–quinoline monomethine cyanine dye has led to the improved detection of RNAs as well as the imaging of nucleolar RNAs in cells. The introduction of an amino-group-terminated side chain into deep-red emissive benzo[c,d]indole–quinoline monomethine cyanine dye has led to the improved detection of RNAs as well as the imaging of nucleolar RNAs in cells.![]()
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Yugo Igarashi
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Michiyuki Suzuki
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Kei Higuchi
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
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12
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Sato T, Sato Y, Nishizawa S. Spectroscopic, thermodynamic and kinetic analysis of selective triplex formation by peptide nucleic acid with double-stranded RNA over its DNA counterpart. Biopolymers 2021; 113:e23474. [PMID: 34478151 DOI: 10.1002/bip.23474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/11/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022]
Abstract
Unlike conventional triplex-forming oligonucleotide (TFO), triplex-forming peptide nucleic acid (PNA) can tightly bind with double-stranded RNA (dsRNA) than double-stranded DNA (dsDNA). Here, we performed spectroscopic, thermodynamic and kinetic experiments for triplex formation by PNA to examine different binding behaviors between PNA - dsRNA and PNA - dsDNA triplexes. We found 9-mer PNA (cytosine content of 66%) formed the thermally stable triplex with dsRNA compared to dsDNA over a wide range of pH (5.5-8.0), salt concentration (50-500 mM NaCl). Both the calorimetric binding constant and the association rate constant for dsRNA were larger than those for dsDNA, indicating the favorable association process for the PNA - dsRNA triplex formation. Comparison with the DNA/RNA heteroduplexes revealed that the DNA strand was detrimental to the triplex stability for PNA, a contrasting result for conventional TFO. The keys underlying the difference in the triplex formation of PNA with different duplexes appear to be the conformational adoptability and the geometric compatibility of PNA to fit the deep, narrow major groove of dsRNA and the helical rigidity difference of the duplexes. Our results emphasize the importance of both the sugar puckering of the duplex and the appropriate conformational flexibility of PNA for the triplex formation.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
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Sato Y, Takahashi Y, Tanabe T, Nishizawa S. Conjugating pyrene onto PNA-based fluorescent probes for improved detection selectivity toward double-stranded siRNA. Org Biomol Chem 2021; 18:4009-4013. [PMID: 32420569 DOI: 10.1039/d0ob00794c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report on the design of new siRNA-binding fluorescent probes with the improved detection selectivity toward intact double-stranded siRNAs over single-stranded forms by the conjugation of pyrene unit into thiazole orange base surrogate-carrying peptide nucleic acid (PNA) that can simultaneously recognize the 3'-overhang and double-stranded sequences of target siRNAs.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
| | - Yuki Takahashi
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
| | - Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
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14
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Lee ETT, Sato Y, Nishizawa S. Small molecule-PNA oligomer conjugates for rRNA A-site at neutral pH for FID assays. Chem Commun (Camb) 2020; 56:14976-14979. [PMID: 33174546 DOI: 10.1039/d0cc06084d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A triplex-forming PNA oligomer conjugated with a naphthyridine derivative (ATMND-C2-NH2) showed high selectivity and strong binding for the bacterial rRNA A-site at pH 7.0 (Kd = 190 ± 72 nM), which was accompanied by fluorogenic signaling that allowed the potential use of this conjugate probe in fluorescent indicator displacement assays.
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Affiliation(s)
- En Ting Tabitha Lee
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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Tohgasaki T, Kondo S, Nishizawa S, Yu X, Ishiwatari S, Sakurai T. 862 Thioredoxin regenerates elastic fibers in the dermis. J Invest Dermatol 2020. [DOI: 10.1016/j.jid.2020.03.878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Sato Y, Kuwahara K, Mogami K, Takahashi K, Nishizawa S. Amphipathic helical peptide-based fluorogenic probes for a marker-free analysis of exosomes based on membrane-curvature sensing. RSC Adv 2020; 10:38323-38327. [PMID: 35517518 PMCID: PMC9057301 DOI: 10.1039/d0ra07763a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/11/2020] [Indexed: 01/08/2023] Open
Abstract
With increasing knowledge about the diverse roles of exosomes in the biological process, much attention has been paid to develop analytical methods for detection and quantification of exosomes. Immunoassays based on the recognition of exosomal protein markers by antibodies were widely used. However, considering that exosomal protein composition varies with the cell type, the protein markers should be carefully selected for a sensitive and selective analysis of target exosomes. Herein, we developed a new class of exosome-binding fluorogenic probes based on membrane curvature (MC) sensing of amphipathic helical (AH) peptides for exosome analysis without the need to use protein markers on the exosomal membranes. The C-terminal region of apolipoprotein A-I labeled with Nile red (ApoC-NR) exhibited a significant fluorescence enhancement upon selective binding to the highly curved membranes of synthetic vesicles. Circular dichroism (CD) measurements involving 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/1-2-dioleoyl-sn-glycerol (DOG) vesicles suggested that ApoC-NR recognizes the lipid packing defects in the surface of highly curved membranes via the hydrophobic insertion of the α-helix structure of the ApoC unit. ApoC-NR exhibited a stronger binding affinity for exosome-sized vesicles and a higher MC selectivity compared to all other previously reported peptide probes. ApoC-NR can be used in a simple and rapid “mix and read” analysis of various kinds of exosomes derived from different cell types (limit of detection: –105 particles/μL) without being influenced by the variation in the expression of the surface proteins of the exosomes, which stands in sharp contrast to immunoassays. Fluorogenic probes based on membrane curvature sensing-amphipathic helical peptides have been developed for a marker-free exosome analysis.![]()
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kazuki Kuwahara
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kenta Mogami
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kenta Takahashi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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17
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Sato Y, Aiba Y, Yajima S, Tanabe T, Higuchi K, Nishizawa S. Cover Feature: Strong Binding and Off–On Signaling Functions of Deep‐Red Fluorescent TO‐PRO‐3 for Influenza A Virus RNA Promoter Region (ChemBioChem 21/2019). Chembiochem 2019. [DOI: 10.1002/cbic.201900621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yusuke Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Yuri Aiba
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Sayaka Yajima
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Takaaki Tanabe
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Kei Higuchi
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
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18
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Yoshino Y, Sato Y, Nishizawa S. Deep-Red Light-up Signaling of Benzo[ c, d]indole-Quinoline Monomethine Cyanine for Imaging of Nucleolar RNA in Living Cells and for Sequence-Selective RNA Analysis. Anal Chem 2019; 91:14254-14260. [PMID: 31595744 DOI: 10.1021/acs.analchem.9b01997] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA-binding small probes with deep-red emission are promising for RNA analysis in biological media without suffering from background fluorescence. Here benzo[c,d]indole-quinoline (BIQ), an asymmetric monomethine cyanine analogue, was newly developed as a novel RNA-selective probe with light-up signaling ability in the deep-red spectral range. BIQ features a significant light-up response (105-fold) with an emission maximum at 657 nm as well as improved photostability over the commercially available RNA-selective probe, SYTO RNA select. BIQ was successfully applied to the fluorescence imaging of nucleolar RNAs in living cells with negligible cytotoxicity. Furthermore, we found the useful ability of BIQ as a base surrogate integrated in peptide nucleic acid (PNA) oligonucleotides for RNA sequence analysis. BIQ base surrogate functioned as a deep-red light-up base surrogate in forced intercalation (FIT) and triplex-forming FIT (tFIT) systems for the sequence-selective detection of single-stranded and double-stranded RNAs, respectively.
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Affiliation(s)
- Yukina Yoshino
- Department of Chemistry, Graduate School of Science , Tohoku University , Japan , Sendai 980-8578 , Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science , Tohoku University , Japan , Sendai 980-8578 , Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science , Tohoku University , Japan , Sendai 980-8578 , Japan
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19
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Sato Y, Aiba Y, Yajima S, Tanabe T, Higuchi K, Nishizawa S. Strong Binding and Off–On Signaling Functions of Deep‐Red Fluorescent TO‐PRO‐3 for Influenza A Virus RNA Promoter Region. Chembiochem 2019; 20:2752-2756. [DOI: 10.1002/cbic.201900331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Yusuke Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Yuri Aiba
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Sayaka Yajima
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Takaaki Tanabe
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Kei Higuchi
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
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20
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Tohgasaki T, Kondo S, Nishizawa S, Suzuki T, Ishiwatari S, Matsukuma S, Ishikawa S, Takeda A. 317 EMILIN-1 is important for age-related changes in elastic fibre structure. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Furuhata Y, Kobayashi M, Maruyama R, Sato Y, Makino K, Michiue T, Yui H, Nishizawa S, Yoshimoto K. Programmable RNA detection with a fluorescent RNA aptamer using optimized three-way junction formation. RNA 2019; 25:590-599. [PMID: 30745364 PMCID: PMC6467008 DOI: 10.1261/rna.069062.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/06/2019] [Indexed: 05/07/2023]
Abstract
RNAs play essential roles in various cellular processes and can be used as biomarkers. Hence, it is important to detect endogenous RNA for understanding diverse cellular functions and diagnosing diseases. To construct a low-cost and easy-to-use RNA detection probe, a chemically unmodified RNA aptamer that binds to a pro-fluorophore to increase its fluorescence is desirable. Here, we focused on Broccoli, a superior variant of Spinach, which is a well-known fluorescent RNA aptamer that binds to DFHBI-1T and emits green fluorescence. We experimentally characterized Broccoli and predicted that it forms a G-quadruplex-based DFHBI-1T recognition region sandwiched between two stems. Based on this, we designed a Broccoli-based RNA detection probe (BRD probe) composed of a sequence of destabilized Broccoli fused with complementary sequences against target RNA. The resulting probe with its target RNA formed a stable three-way junction, named the MT2 three-way junction, which contributed to efficient refolding of the Broccoli structure and allowed for programmable RNA detection with high signal-to-noise ratio and sensitivity. Interestingly, the MT2 three-way junction also could be applied to probe construction of a truncated form of Spinach (Baby Spinach). The BRD and Baby Spinach-based RNA detection probes (BSRD probe) exhibited up to 48- and 140-fold fluorescence enhancements in the presence of their target RNAs and detected small amounts of target RNA that were as low as 160 and 5 nM, respectively. Thus, we experimentally characterized the higher order structure of Broccoli and developed structure-switching aptamer probes for highly sensitive, programmable, RNA detection using an MT2 three-way junction.
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Affiliation(s)
- Yuichi Furuhata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Mizuki Kobayashi
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan
| | - Ryo Maruyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kurumi Makino
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Hiroharu Yui
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- JST, PRESTO, The University of Tokyo, Tokyo 153-8902, Japan
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22
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Sato T, Sakamoto N, Nishizawa S. Kinetic and thermodynamic analysis of triplex formation between peptide nucleic acid and double-stranded RNA. Org Biomol Chem 2019; 16:1178-1187. [PMID: 29376179 DOI: 10.1039/c7ob02912h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Kinetics and thermodynamics of triplex formation between 9-mer homopyrimidine PNA (H2N-Lys-TCTCCTCCC-CONH2) and double-stranded RNA (dsRNA, 5'-AGAGGAGGG-3'/3'-UCUCCUCCC-5') at acidic pH were studied by means of a stopped-flow technique and isothermal titration calorimetry (ITC). These results revealed the following main findings: (i) the stable PNA-dsRNA triplex formation mostly originated from the large association rate constant (kon), which was dominated by both the charge neutral PNA backbone and the protonation level of the PNA cytosine. (ii) The temperature dependence of the enthalpy change (ΔH) and kon suggested that the association phase of the PNA-dsRNA triplex formation comprised a non-directional nucleation-zipping mechanism that was coupled with the conformational transition of the unbound PNA. (iii) The destabilization by a mismatch in the dsRNA sequence mainly resulted from the decreased magnitude of both kon and ΔH. (iv) There was sequence and position dependence of the mismatch on ΔH and the activation energy (Eon), which illustrated the importance of base pairing in the middle of the sequence. Our results for the first time revealed an association mechanism for the PNA-dsRNA triplex formation. A set of the kinetic and thermodynamic data we reported here will also expand the scope of understanding for nucleic acid recognition by PNA.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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23
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Sato Y, Yajima S, Taguchi A, Baba K, Nakagomi M, Aiba Y, Nishizawa S. Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA. Chem Commun (Camb) 2019; 55:3183-3186. [DOI: 10.1039/c9cc00414a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report that TO-PRO-3 functions as a deep-red fluorescent indicator for the internal loop structure of the bacterial (Escherichia coli) A-site, which enables the assessment of A-site binding capability of various test compounds including blue and even-green-emitting compounds.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Sayaka Yajima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Akifumi Taguchi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kyosuke Baba
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Mayu Nakagomi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yuri Aiba
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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24
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Tanabe T, Sato T, Sato Y, Nishizawa S. Design of a fluorogenic PNA probe capable of simultaneous recognition of 3'-overhang and double-stranded sequences of small interfering RNAs. RSC Adv 2018; 8:42095-42099. [PMID: 35558768 PMCID: PMC9092112 DOI: 10.1039/c8ra08759h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/09/2018] [Indexed: 11/21/2022] Open
Abstract
We developed a new fluorescent peptide nucleic acid (PNA) probe, COT probe, capable of simultaneous recognition of 3'-overhang and double stranded sequences of target small interfering RNA (siRNA).
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Affiliation(s)
- Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
| | - Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University Sendai 980-8578 Japan +81-22-795-6549 +81-22-795-6552
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25
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Sato Y, Kaneko M, Sato T, Nakata S, Takahashi Y, Nishizawa S. Enhanced Binding Affinity of siRNA Overhang‐Binding Fluorescent Probes by Conjugation with Cationic Oligopeptides for Improved Analysis of the siRNA Delivery Process. Chembiochem 2018; 20:408-414. [DOI: 10.1002/cbic.201800560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Yusuke Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Mitsumasa Kaneko
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Takaya Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Saki Nakata
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Yuki Takahashi
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
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26
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Sato Y, Iwasawa D, Hui KP, Nakagomi R, Nishizawa S. Improved Boronate Affinity Electrophoresis by Optimization of the Running Buffer for a Single-step Separation of piRNA from Mouse Testis Total RNA. ANAL SCI 2018; 34:627-630. [PMID: 29743438 DOI: 10.2116/analsci.17n024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here we examined optimization of the running buffer in boronate affinity electrophoresis for improved separation of PIWI-interacting RNA (piRNA) with 2'-O-methylated ribose in 3'-terminal nucleotide. The use of Good's buffer, such as HEPES, significantly increased the separation efficiency for piRNA over normal RNA with free 3'-terminal ribose, and retained an ability to resolve the difference by at least 4-nucleotide lengths in the target piRNAs. We also demonstrated a single-step separation of piRNA from mouse testis total RNA.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Daijiro Iwasawa
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Kuo Ping Hui
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Rena Nakagomi
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University
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27
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Masuda T, Shibuya Y, Arai S, Kobayashi S, Suzuki S, Kijima J, Itoh T, Sato Y, Nishizawa S, Yamaguchi A. Effect of Cavity Size of Mesoporous Silica on Short DNA Duplex Stability. Langmuir 2018; 34:5545-5550. [PMID: 29715034 DOI: 10.1021/acs.langmuir.8b00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We studied the stabilities of short (4- and 3-bp) DNA duplexes within silica mesopores modified with a positively charged trimethyl aminopropyl (TMAP) monolayer (BJH pore diameter 1.6-7.4 nm). The DNA fragments with fluorescent dye were introduced into the pores, and their fluorescence resonance energy transfer (FRET) response was measured to estimate the structuring energies of the short DNA duplexes under cryogenic conditions (temperature 233-323 K). The results confirmed the enthalpic stability gain of the duplex within size-matched pores (1.6 and 2.3 nm). The hybridization equilibrium constants found for the size-matched pores were 2 orders of magnitude larger than those for large pores (≥3.5 nm), and this size-matching effect for the enhanced duplex stability was explained by a tight electrostatic interaction between the duplex and the surface TMAP groups. These results indicate the requirement of the precise regulation of mesopore size to ensure the stabilization of hydrogen-bonded supramolecular assemblies.
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Affiliation(s)
- Tsubasa Masuda
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Yuuta Shibuya
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Shota Arai
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Sayaka Kobayashi
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Sotaro Suzuki
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Jun Kijima
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
| | - Tetsuji Itoh
- Research Institute for Chemical Process Technology , National Institute of Advanced Industrial Science and Technology (AIST) , Nigatake 4-2-1 , Sendai 983-8551 , Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Akira Yamaguchi
- Institute of Quantum Beam Science , Ibaraki University , 2-1-1 Bunkyo , Mito , Ibaraki 310-8512 , Japan
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Chiba T, Sato T, Sato Y, Nishizawa S. Red-emissive triplex-forming PNA probes carrying cyanine base surrogates for fluorescence sensing of double-stranded RNA. Org Biomol Chem 2018; 15:7765-7769. [PMID: 28905972 DOI: 10.1039/c7ob02077e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Red-emissive fluorescent probes have been developed by integration of quinoline blue or thiazole red as the base surrogate into triplex-forming PNAs, allowing selective sensing of a sequence of double-stranded RNA.
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Affiliation(s)
- Toshiki Chiba
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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29
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Suzuki T, Shibuya Y, Sato T, Nishizawa S, Sato I, Yamaguchi A. Thermodynamics of Complexation between Thiourea-based Receptor and Acetate in Water/Acetonitrile Mixture. ANAL SCI 2018; 32:741-4. [PMID: 27396654 DOI: 10.2116/analsci.32.741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A thiourea-based receptor has been extensively studied for selective anion recognition for reasons of its strong hydrogen bond donor ability. In the present study, the thermodynamics of complexation between a thiourea-based receptor and acetate was examined in a water/acetonitrile mixture. The receptor used in this study was N,N'-bis(p-nitrophenyl)thiourea (BNPTU). UV/vis spectroscopic titration and isothermal titration calorimetry (ITC) experiments clearly revealed endothermic and entropy-driven complexation of BNPTU with acetate in water/acetonitrile mixtures. Since the endothermic peaks found in water/acetonitrile mixtures were about three times greater than those in acetonitrile, it appears that preferential hydration of both receptor and acetate was responsible for the endothermic and entropy-driven complexation reaction. The thermodynamic properties found in this study have the potential to contribute to the design of a thiourea-based anion receptor.
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30
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Hisanaga S, Kakeda S, Yamamoto J, Watanabe K, Moriya J, Nagata T, Fujino Y, Kondo H, Nishizawa S, Korogi Y. Pituitary Macroadenoma and Visual Impairment: Postoperative Outcome Prediction with Contrast-Enhanced FIESTA. AJNR Am J Neuroradiol 2017; 38:2067-2072. [PMID: 28912278 DOI: 10.3174/ajnr.a5394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/06/2017] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Contrast-enhanced FIESTA can depict anterior optic pathways in patients with large suprasellar tumors. We assessed whether the degree of kink in the optic nerve at the optic canal orifice on contrast-enhanced FIESTA correlates with the postoperative improvement of visual impairment in patients with pituitary macroadenoma. MATERIALS AND METHODS Thirty-one patients with pituitary macroadenoma who underwent preoperative MR imaging and an operation were evaluated. We measured the optic nerve kinking angle on sagittal oblique contrast-enhanced FIESTA parallel to the optic nerve; the optic nerve kinking angle was defined as the angle between a line parallel to the planum sphenoidale and a line parallel to the intracranial optic nerve at the optic canal orifice. We used logistic regression analyses to determine whether the clinical (sex, age, and duration of symptoms) and imaging (tumor height, chiasmal compression severity, hyperintense optic nerve on T2WI, and optic nerve kinking angle) characteristics were associated with the postoperative improvement (good-versus-little improvement) of visual acuity disturbance and visual field defect. RESULTS There were 53 impaired sides before the operation: 2 sides with visual acuity disturbance alone, 25 with visual field defect alone, and 26 with both. After the operation, good improvement was found in 17 of the 28 sides with visual acuity disturbance and in 32 of the 51 sides with visual field defects. Only the optic nerve kinking angle was significantly associated with good improvement of the visual acuity disturbance (P = .011) and visual field defect (P = .002). CONCLUSIONS The degree of the optic nerve kinking angle was an independent predictor of postoperative improvement, indicating that irreversible damage to the optic nerve may be associated with its kinking at the optic canal orifice.
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Affiliation(s)
- S Hisanaga
- From the Departments of Radiology (S.H., S.K., K.W., J.M., Y.K.)
| | - S Kakeda
- From the Departments of Radiology (S.H., S.K., K.W., J.M., Y.K.)
| | | | - K Watanabe
- From the Departments of Radiology (S.H., S.K., K.W., J.M., Y.K.)
| | - J Moriya
- From the Departments of Radiology (S.H., S.K., K.W., J.M., Y.K.)
| | | | - Y Fujino
- Preventive Medicine and Community (Y.F.), University of Occupational and Environmental Health School of Medicine, Kitakyushu, Japan
| | | | | | - Y Korogi
- From the Departments of Radiology (S.H., S.K., K.W., J.M., Y.K.)
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Sakata-Yanagimoto M, Fujisawa M, Nishizawa S, Komori D, Gershon P, Kiryu M, Swarna T, Fukumoto K, Enami T, Muratani M, Yoshida K, Ogawa S, Matsue K, Nakamura N, Takeuchi K, Izutsu K, Teshima T, Fujimoto K, Miyoshi H, Gaulard P, Ohshima K, Chiba S. ACTIVATION OF RHOA-VAV1 SIGNALING IN ANGIOIMMUNOBLASTIC T-CELL LYMPHOMA. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - M. Fujisawa
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - S. Nishizawa
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - D. Komori
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - P. Gershon
- Department of Molecular Biology& Biochemistry; UC-Irvine; California USA
| | - M. Kiryu
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - T. Swarna
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - K. Fukumoto
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - T. Enami
- Department of Hematology; University of Tsukuba; Ibaraki Japan
| | - M. Muratani
- Department of Genome Biology; University of Tsukuba; Ibaraki Japan
| | - K. Yoshida
- Department of Pathology and Tumor Biology; Kyoto University; Kyoto Japan
| | - S. Ogawa
- Department of Pathology and Tumor Biology; Kyoto University; Kyoto Japan
| | - K. Matsue
- Division of Hematology/Oncology, Department of Internal Medicine; Kameda Medical Center; Chiba Japan
| | - N. Nakamura
- Department of Pathology; Tokai University School of Medicine; Kanagawa Japan
| | - K. Takeuchi
- Pathology Project for Molecular Targets, The Cancer Institute; Japanese Foundation for Cancer Research; Tokyo Japan
| | - K. Izutsu
- Department of Hematology; Toranomon Hospital; Tokyo Japan
| | - T. Teshima
- Department of Hematology; Hokkaido University Graduate School of Medicine; Sapporo Japan
| | - K. Fujimoto
- Department of Hematology; Hokkaido University Graduate School of Medicine; Sapporo Japan
| | - H. Miyoshi
- Department of Pathology; University of Kurume; Fukuoka Japan
| | - P. Gaulard
- Département de Pathologie & Inserm U955; Hôpital Henri Mondor; Créteil France
| | - K. Ohshima
- Department of Pathology; University of Kurume; Fukuoka Japan
| | - S. Chiba
- Department of Hematology; University of Tsukuba; Ibaraki Japan
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32
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Nishizawa S. Cross-Cultural Effects on Hemispheric Specialization Reflected on a Task Requiring Spatial Discrimination of the Thumb by Japanese and American Students. Percept Mot Skills 2017; 78:771-6. [PMID: 8084689 DOI: 10.1177/003151259407800317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Difference limens and constant errors were obtained by the method of constant stimuli on a task requiring discrimination of the thumb's spatial position for 26 Japanese (13 male and 13 female) and 26 American (13 male and 13 female) college students. The left thumbs of Japanese and American subjects exhibited smaller difference limens, suggesting that both groups show the same hemispheric specialization of spatial perception. Japanese subjects showed smaller difference limens, but no sex difference was observed.
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Sato T, Sato Y, Nishizawa S. Inside Back Cover: Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA (Chem. Eur. J. 17/2017). Chemistry 2017. [DOI: 10.1002/chem.201605678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Takaya Sato
- Department of Chemistry; Graduate School of Science; Tohoku University; Sendai 980-8578 Japan
| | - Yusuke Sato
- Department of Chemistry; Graduate School of Science; Tohoku University; Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of Chemistry; Graduate School of Science; Tohoku University; Sendai 980-8578 Japan
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34
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Sato T, Sato Y, Nishizawa S. Correction to “Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA”. J Am Chem Soc 2017; 139:3567. [DOI: 10.1021/jacs.7b01636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Sato T, Sato Y, Nishizawa S. Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA. Chemistry 2017; 23:4079-4088. [PMID: 27897343 DOI: 10.1002/chem.201604676] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 12/24/2022]
Abstract
A series of triplex-forming peptide nucleic acid (TFP) probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found that the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base. Isothermal titration calorimetry experiments revealed that the increased binding affinity resulted from the gain in the binding enthalpy, which could be explained by the enhanced π-stacking interaction between the TO base surrogate and the dsRNA part of the triplex. We expect that these results will provide a molecular basis for designing strong binding tFIT probes for fluorescence sensing of various kinds of purine-rich dsRNAs sequences including those carrying a pyrimidine-purine inversion. The obtained data also offers a new insight into further development of the universal bases incorporated in TFP.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
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36
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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37
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Hoshi K, Fujihara Y, Mori Y, Asawa Y, Kanazawa S, Nishizawa S, Misawa M, Numano T, Inoue H, Sakamoto T, Watanabe M, Komura M, Takato T. Production of three-dimensional tissue-engineered cartilage through mutual fusion of chondrocyte pellets. Int J Oral Maxillofac Surg 2016; 45:1177-85. [DOI: 10.1016/j.ijom.2016.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 08/07/2015] [Accepted: 03/02/2016] [Indexed: 10/21/2022]
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38
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Sato Y, Asami T, Toriyabe Y, Sato T, Teramae N, Nishizawa S. Pteridine Derivatives Modified with a Guanidine for Binding and Sensing an Orphan Guanine in RNA Duplexes. CHEM LETT 2016. [DOI: 10.1246/cl.160425] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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39
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Sato T, Sato Y, Nishizawa S. Triplex-Forming Peptide Nucleic Acid Probe Having Thiazole Orange as a Base Surrogate for Fluorescence Sensing of Double-stranded RNA. J Am Chem Soc 2016; 138:9397-400. [PMID: 27442229 DOI: 10.1021/jacs.6b05554] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
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40
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Araki S, Gao B, Nishizawa S, Nakano S, Kakimoto K. Total pressure-controlled PVT SiC growth for polytype stability during using 2D nucleation theory. Crystal Research and Technology 2016. [DOI: 10.1002/crat.201500344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- S. Araki
- Department of Aeronautics and Astronautics; Kyushu University; 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - B. Gao
- Research Institute for Applied Mechanics; Kyushu University; 6-1 Kasuga-koen Kasuga Fukuoka 816-8580 Japan
| | - S. Nishizawa
- National Institute of Advanced Industrial Science and Technology; 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan
| | - S. Nakano
- Research Institute for Applied Mechanics; Kyushu University; 6-1 Kasuga-koen Kasuga Fukuoka 816-8580 Japan
| | - K. Kakimoto
- Department of Aeronautics and Astronautics; Kyushu University; 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
- Research Institute for Applied Mechanics; Kyushu University; 6-1 Kasuga-koen Kasuga Fukuoka 816-8580 Japan
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41
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Sato T, Sato Y, Iwai K, Kuge S, Teramae N, Nishizawa S. Fluorescence imaging of siRNA delivery by peptide nucleic acid-based probe. ANAL SCI 2016; 31:315-20. [PMID: 25864675 DOI: 10.2116/analsci.31.315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report on the use of a peptide nucleic acid (PNA)-based fluorescent probe for the analysis of siRNA delivery to living cells. The probe, Py-AA-TO, possesses thiazole orange (TO) and pyrene moieties in the C- and N-termini of PNA, and can function as a light-up probe capable of selective binding to 3'-overhanging nucleotides of target siRNAs. The affinity-labeling of the siRNAs with Py-AA-TO facilitates fluorescence imaging of cellular uptake of polymer-based carriers encapsulating the siRNAs (polyplexes) through endocytosis and subsequent sequestration into lysosome. In addition, flow cytometric measurements reveal that the monitoring of Py-AA-TO fluorescence inside the cells is successfully applicable to the analysis of the polyplex disassembly. These promising functions of Py-AA-TO are presented and discussed as a basis for the design of molecular probes for fluorescent imaging and quantitative analysis of the siRNA delivery process.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University
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42
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Sato T, Sato Y, Iwai K, Kuge S, Nishizawa S, Teramae N. Synthetic fluorescent probes capable of selective recognition of 3'-overhanging nucleotides for siRNA delivery imaging. Chem Commun (Camb) 2015; 51:1421-4. [PMID: 25483137 DOI: 10.1039/c4cc08800j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Peptide nucleic acid (PNA)-thiazole orange (TO) conjugates are developed as fluorescent probes capable of selective recognition of 3'-overhanging nucleotides of siRNAs for an accurate analysis of the siRNA delivery process.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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43
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Sato Y, Sato T, Sato T, Nishizawa S, Teramae N. The effect of LNA nucleobases as enhancers for the binding of amiloride to an abasic site in DNA/DNA and DNA/RNA duplexes. Org Biomol Chem 2015; 12:7250-6. [PMID: 25101634 DOI: 10.1039/c4ob00977k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report on a significant effect of locked nucleic acid (LNA) nucleobases on the binding of amiloride for abasic site (AP)-containing DNA duplexes. Fluorescence titration experiments showed that the binding affinity of amiloride for the target thymine (T) opposite an AP site significantly improves for the DNA duplexes possessing LNA nucleobases that flank the AP site, compared to the corresponding normal DNA duplexes. In particular, LNA flanking nucleobases on both 5'- and 3'-sides of the AP site are found to be effective for the enhancement of the binding affinity. From thermodynamic characterization of the amiloride binding, the loss in the binding entropy is remarkably reduced for the LNA-containing DNA duplexes, which is indeed responsible for the enhanced affinity of amiloride. Moreover, such an effect of LNA nucleobases was also observed for amiloride binding to DNA/RNA hybrid duplexes.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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Furuna T, Nagasaki H, Nishizawa S, Sugiura M, Okuzumi H, Ito H, Kinugasa T, Hashizume K, Maruyama H. Longitudinal change in the physical performance of older adults in the community. J Jpn Phys Ther Assoc 2015; 1:1-5. [PMID: 25792874 DOI: 10.1298/jjpta.1.1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/1997] [Accepted: 02/07/1998] [Indexed: 01/26/2023]
Abstract
The primary purposes of this study were 1) to confirm age-related deterioration of physical performance in older adults longitudinally, and 2) to predict future functional status and mortality by initial level of physical performances. The subjects were 517 older adults examined both in 1992 and 1996 in the Tokyo Metropolitan Institute of Gerontology, Longitudinal Interdisciplinary Study on Aging. The same battery consisting of muscle strength, balance, walking, and manual speed was administered to the subjects in the baseline and follow-up examinations. A significant longitudinal decline was observed in all physical performances except for grip strength. The age-related decline accelerated with aging for preferred walking velocity. Inter-subject variability in walking velocity significantly increased for 4 years period. Maximum walking velocity was a common predictor for functional status and mortality. The results suggest that physical performance measures, especially maximum walking velocity, is a valid means for physical therapy to evaluate physical functioning of community-living older persons.
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Affiliation(s)
- T Furuna
- Department of Kinesiology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - H Nagasaki
- Department of Kinesiology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - S Nishizawa
- Department of Kinesiology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - M Sugiura
- Department of Kinesiology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
| | - H Okuzumi
- The Research Institute for the Education of Exceptional Children, Tokyo Gakugei University, Tokyo 184-0015, Japan
| | - H Ito
- Department of Physical Therapy, Ibaraki Prefectural University of Health Science, Ibaraki 300-0301, Japan
| | - T Kinugasa
- College of Medical Technology and Nursing, University of Tsukuba, Ibaraki 305-0006, Japan
| | - K Hashizume
- Faculty of Health and Sports Sciences, Osaka University, Osaka 560-0006, Japan
| | - H Maruyama
- Department of Physical Therapy, International University of Medicine and Welfare, Tochigi 324-0011, Japan
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45
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Tao J, Song P, Sato Y, Nishizawa S, Teramae N, Tong A, Xiang Y. A label-free and sensitive fluorescent method for the detection of uracil-DNA glycosylase activity. Chem Commun (Camb) 2015; 51:929-32. [DOI: 10.1039/c4cc06170e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A label-free fluorescent method has been developed for sensitive detection of uracil-DNA glycosylase activity as well as UDG inhibitors.
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Affiliation(s)
- Jing Tao
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 100084
| | - Panshu Song
- National Institute of Metrology
- Beijing 100029
- China
| | - Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Norio Teramae
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Aijun Tong
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 100084
| | - Yu Xiang
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 100084
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46
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Sato Y, Kudo M, Toriyabe Y, Kuchitsu S, Wang CX, Nishizawa S, Teramae N. Abasic site-binding ligands conjugated with cyanine dyes for “off–on” fluorescence sensing of orphan nucleobases in DNA duplexes and DNA–RNA hybrids. Chem Commun (Camb) 2014; 50:515-7. [DOI: 10.1039/c3cc47717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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47
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Ko E, Fujihara Y, Ogasawara T, Asawa Y, Nishizawa S, Watanabe M, Nagata S, Yang C, Takato T, Hoshi K. The BMP family and the importance of insulin in chondrogenesis: could we substitute BMP-2 with BMP-4 for the tissue engineering of cartilage. Int J Oral Maxillofac Surg 2013. [DOI: 10.1016/j.ijom.2013.07.730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Yamamoto J, Kakeda S, Shimajiri S, Takahashi M, Watanabe K, Kai Y, Moriya J, Korogi Y, Nishizawa S. Tumor consistency of pituitary macroadenomas: predictive analysis on the basis of imaging features with contrast-enhanced 3D FIESTA at 3T. AJNR Am J Neuroradiol 2013; 35:297-303. [PMID: 23928139 DOI: 10.3174/ajnr.a3667] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Preoperative evaluation of pituitary macroadenoma tumor consistency is important for neurosurgery. Thus, we aimed to retrospectively assess the role of contrast-enhanced FIESTA in predicting the tumor consistency of pituitary macroadenomas. MATERIALS AND METHODS Twenty-nine patients with pituitary macroadenomas underwent conventional MR imaging sequences and contrast-enhanced FIESTA before surgery. Two neuroradiologists assessed the contrast-enhanced FIESTA, contrast-enhanced T1WI, and T2WI. On the basis of surgical findings, the macroadenomas were classified by the neurosurgeons as either soft or hard. Finally, Fisher exact probability tests and unpaired t tests were used to compare predictions on the basis of the MR imaging findings with the tumor consistency, collagen content, and postoperative tumor size. RESULTS The 29 pituitary macroadenomas were classified as either solid or mosaic types. Solid type was characterized by a homogeneous pattern of tumor signal intensity without intratumoral hyperintense dots, whereas the mosaic type was characterized by many intratumoral hyperintense dots on each MR image. Statistical analyses revealed a significant correlation between tumor consistency and contrast-enhanced FIESTA findings. Sensitivity and specificity were higher for contrast-enhanced FIESTA (1.00 and 0.88-0.92, respectively) than for contrast-enhanced T1WI (0.80 and 0.25-0.33, respectively) and T2WI (0.60 and 0.38-0.54, respectively). Compared with mosaic-type adenomas, solid-type adenomas tended to have a hard tumor consistency as well as a significantly higher collagen content and lower postoperative tumor size. CONCLUSIONS Contrast-enhanced FIESTA may provide preoperative information regarding the consistency of macroadenomas that appears to be related to the tumor collagen content.
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Affiliation(s)
- J Yamamoto
- From the Departments of Neurosurgery (J.Y., M.T., K.W., S.N.)
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49
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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Back Cover: Rational Design for Cooperative Recognition of Specific Nucleobases Using β-Cyclodextrin-Modified DNAs and Fluorescent Ligands on DNA and RNA Scaffolds (Chem. Eur. J. 32/2013). Chemistry 2013. [DOI: 10.1002/chem.201390120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds. Chemistry 2013; 19:10526-35. [PMID: 23821253 DOI: 10.1002/chem.201300985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/10/2023]
Abstract
We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
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Affiliation(s)
- Akika Futamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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