1
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Kaku T, Ikebukuro K, Tsukakoshi K. Structure of cytotoxic amyloid oligomers generated during disaggregation. J Biochem 2024:mvae023. [PMID: 38430131 DOI: 10.1093/jb/mvae023] [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] [Received: 08/30/2023] [Revised: 02/05/2024] [Indexed: 03/03/2024] Open
Abstract
Amyloidosis is characterized by the abnormal accumulation of amyloid proteins. The causative proteins aggregate from monomers to oligomers and fibrils, among which some intermediate oligomers considered as major toxins. Cytotoxic oligomers are generated not only by aggregation but also via fibril disaggregation. However, little is known about the structural characteristics and generation conditions of cytotoxic oligomers produced during disaggregation. Herein, we summarized the structural commonalities of cytotoxic oligomers formed under various disaggregation conditions, including the addition of heat shock proteins or small compounds. In vitro experimental data demonstrated the presence of high-molecular-weight oligomers (protofibrils or protofilaments) that exhibited a fibrous morphology and β-sheet structure. Molecular dynamics simulations indicated that the distorted β-sheet structure contributed to their metastability. The tendency of these cytotoxic oligomers to appear under mild disaggregation conditions, implied formation during the early stages of disaggregation. This review will aid researchers in exploring the characteristics of highly cytotoxic oligomers and developing drugs that target amyloid aggregates.
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Affiliation(s)
- Toshisuke Kaku
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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2
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Komiya E, Takamatsu S, Miura D, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K, Asano R. Exploration and Application of DNA-Binding Proteins to Make a Versatile DNA-Protein Covalent-Linking Patch (D-Pclip): The Case of a Biosensing Element. J Am Chem Soc 2024; 146:4087-4097. [PMID: 38295327 PMCID: PMC10870700 DOI: 10.1021/jacs.3c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
DNA-protein complexes are attractive components with broad applications in various research fields, such as DNA aptamer-enzyme complexes as biosensing elements. However, noncovalent DNA-protein complexes often decrease detection sensitivity because they are highly susceptible to environmental conditions. In this study, we developed a versatile DNA-protein covalent-linking patch (D-Pclip) for fabricating covalent and stoichiometric DNA-protein complexes. We comprehensively explored the database to determine the DNA-binding ability of the candidates and selected UdgX as the only uracil-DNA glycosylase known to form covalent bonds with DNA via uracil, with a binding efficiency >90%. We integrated a SpyTag/SpyCatcher protein-coupling system into UdgX to create a universal and convenient D-Pclip. The usability of D-Pclip was shown by preparing a stoichiometric model complex of a hemoglobin (Hb)-binding aptamer and glucose oxidase (GOx) by mixing at 4 °C. The prepared aptamer-GOx complexes detected Hb in a dose-dependent manner within the clinically required detection range in buffer and human serum without any washing procedures. D-Pclip covalently connects any uracil-inserted DNA sequence and any SpyCatcher-fused protein stoichiometrically; therefore, it has a high potential for various applications.
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Affiliation(s)
- Erika Komiya
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shouhei Takamatsu
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daimei Miura
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wakako Tsugawa
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint
Department of Biomedical Engineering, University
of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
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3
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Rokutani S, Hiraka K, Saitoh H, Saito T, Nonaka Y, Ueno K, Tsukakoshi K, Ohnishi N, Ikebukuro K. Aptamer-enhanced particle aggregation inhibition assay for simple homogeneous protein detection using DNA aptamer and thermo-responsive magnetic nanoparticles. Biosens Bioelectron 2024; 245:115827. [PMID: 37979546 DOI: 10.1016/j.bios.2023.115827] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
A simple and sensitive homogeneous protein detection system is required for the early detection of biomarkers. Thermo-responsive magnetic particles (TM) have already been developed to achieve easy bound/free separation at the homogeneous protein detection system, but they are still limited owing to the requirement of secondary antibodies and negatively charged polymers, and it is challenging to control the TM aggregation behavior because of the size of the TM. Therefore, at new method to control TM aggregation behavior that is simple, easy, and highly sensitive is required. In this study, we developed a DNA aptamer-based TM assay as a simple protein detection system without additional secondary molecular recognition elements or negatively charged polymer. In the first attempt, a DNA aptamer was modified on the TM surface, and its aggregation behavior was monitored depending on the target molecule concentration. The TM aggregation rate during the heating process decreased depending on the amount of the DNA aptamer and increased depending on the target protein level. This suggests that the DNA aptamer prevented TM aggregation owing to its negative charge and achieved target protein detection owing to the cancellation of repulsion. Capturable aptamers were used in the TM assay to improve the sensitivity and limit of detection. The designed Capture DNA was modified on the TM surface, and the aptamer was captured in the presence of the target protein through a conformational change. Eventually, Capturable aptamer-based TM assay achieved a sub-nanomolar limit of detection and higher sensitivity than that of our initial investigation. Through this study and the ease of the DNA aptamer design, it was shown that the DNA aptamer-modified TM assay enabled the development of a simple and sensitive homogeneous protein detection system.
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Affiliation(s)
- Shunsuke Rokutani
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kentaro Hiraka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan; College of Science, Engineering and Technology, Grand Canyon University, 3300 W Camelback Rd, Phoenix, AZ, 85017, USA; National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Hiroshi Saitoh
- JNC Petrochemical Corporation, Goi Research Center, 5-1 Goi-kaigan, Ichihara, Chiba, 290-8551, Japan
| | - Taiki Saito
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yoshihiko Nonaka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kinuko Ueno
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Noriyuki Ohnishi
- JNC Petrochemical Corporation, Goi Research Center, 5-1 Goi-kaigan, Ichihara, Chiba, 290-8551, Japan.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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4
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Numaguchi Y, Tsukakoshi K, Takeuchi N, Suzuki Y, Ikebukuro K, Kawano R. Real-time monitoring of the amyloid β 1-42 monomer-to-oligomer channel transition using a lipid bilayer system. PNAS Nexus 2024; 3:pgad437. [PMID: 38156289 PMCID: PMC10753159 DOI: 10.1093/pnasnexus/pgad437] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 12/30/2023]
Abstract
This study describes the observation of the transformation of monomeric amyloid β1-42 (Aβ42) into oligomers in a lipid membrane utilizing a lipid bilayer system for electrophysiological measurement. The relevance of oligomers and protofibrils in Alzheimer's disease (AD) is underscored given their significant neurotoxicity. By closely monitoring the shift of Aβ42 from its monomeric state to forming oligomeric channels in phospholipid membranes, we noted that this transformation transpired within a 2-h frame. We manipulated the lipid membrane's constitution with components such as glycerophospholipid, porcine brain total lipid extract, sphingomyelin (SM), and cholesterol (Chol.) to effectively imitate nerve cell membranes. Interesting findings showcased Chol.'s ability to foster stable oligomeric channel formation in the lipid membrane, with SM and GM1 lipids potentially enhancing channel formation as well. Additionally, the study identified the potential of a catechin derivative, epigallocatechin gallate (EGCG), in obstructing oligomerization. With EGCG present in the outer solution of the Aβ42-infused membrane, a noteworthy reduction in channel current was observed, suggesting the successful inhibition of oligomerization. This conclusion held true in both, prior and subsequent, stages of oligomerization. Our findings shed light on the toxicity of oligomers, promising invaluable information for future advancements in AD treatment strategies.
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Affiliation(s)
- Yuri Numaguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Nanami Takeuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Yuki Suzuki
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Mie 514-0102, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-0011, Japan
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5
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Todoroki K, Hamada D, Yamada T, Saito T, Shimizu Y, Sugiyama E, Mizuno H, Hayashi H, Tsukakoshi K, Ikebukuro K. Development of a liquid chromatography-based versatile bioanalysis for bevacizumab based on pretreatment combining aptamer affinity purification and centrifugal ultrafiltration concentration. ANAL SCI 2023; 39:1805-1811. [PMID: 37660341 DOI: 10.1007/s44211-023-00417-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023]
Abstract
We report on the development of a versatile and accurate bioanalytical method for bevacizumab using a pretreatment method combining affinity purification with anti-idiotypic DNA aptamers and centrifugal ultrafiltration concentration, followed by liquid chromatography (LC)-fluorescence analysis. An affinity purification method using Sepharose beads as an affinity support removed immunoglobulin G and a large amount of coexisting substances in the serum sample. Purified bevacizumab was separated as a single peak by conventional LC and detected fluorometrically, showing good linearity (R2 = 0.999) in the range of 5-200 μg/mL, sufficient to analyze bevacizumab concentrations in the blood of bevacizumab-treated patients. By combining this purification method with a concentration method using a centrifugal filtration device that inhibits non-specific adsorption of bevacizumab, the quantitative range was reduced by a factor of 10 while showing good linearity (R2 = 0.999) in the 0.5-20 μg/mL range. The developed analytical method is expected to be used not only for general bioanalysis of therapeutic mAbs in clinical settings, but also for next-generation antibody drugs that show drug efficacy at low concentrations and for analysis of trace samples.
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Affiliation(s)
- Kenichiro Todoroki
- Department of Analytical and Bioanalytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1, Yada, Suruga-Ku, Shizuoka, 422-8526, Japan.
| | - Daichi Hamada
- Department of Analytical and Bioanalytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1, Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Tomohiro Yamada
- Department of Analytical and Bioanalytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1, Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Taro Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Japan
| | - Yutaka Shimizu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Japan
| | - Eiji Sugiyama
- Department of Analytical and Bioanalytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1, Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Hajime Mizuno
- Laboratory of Analytical Chemistry, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku, Nagoya, 468-8503, Japan
| | - Hideki Hayashi
- Laboratory of Community Pharmaceutical Practice and Science, Gifu Pharmaceutical University, Daigaku-Nishi 1-25-4, Gifu, 501-1196, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Japan
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6
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Murakami T, Kaku T, Tsukakoshi K, Iwaide S, Itoh Y, Hisada M, Nomura K, Kubo R, Ikebukuro K, Sassa-O'Brien Y, Kametani F. Identification of novel amyloidosis in dogs: α-S1-casein acquires amyloidogenicity in mammary tumor by overexpression and N-terminal truncation. Vet Pathol 2023; 60:203-213. [PMID: 36680468 DOI: 10.1177/03009858221148511] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 01/22/2023]
Abstract
Mammary tumor-associated amyloidosis (MTAA) in dogs is characterized by amyloid deposition in the stroma of mammary adenoma or carcinoma; however, the amyloid precursor protein remains unknown. We attempted to identify an amyloid precursor protein and elucidated its etiology by characterizing 5 cases of canine MTAA. Proteomic analyses of amyloid extracts from formalin-fixed paraffin-embedded specimens revealed α-S1-casein (CASA1) as a prime candidate and showed the N-terminal truncation of canine CASA1. Both immunohistochemistry and immunoelectron microscopy showed that amyloid deposits or fibrils in MTAA cases were positive for CASA1. Reverse transcription-polymerase chain reaction and quantitative polymerase chain reaction revealed the complete mRNA sequence encoding CASA1, whose expression was significantly higher in the amyloid-positive group. The recombinant protein of the N-terminal-truncated canine CASA1 and the synthetic peptides derived from canine and human CASA1 formed amyloid-like fibrils in vitro. Structural prediction suggested that the N-terminal region of CASA1 was disordered. Previously, full-length CASA1 was reported to inhibit the amyloidogenesis of other proteins; however, we demonstrated that CASA1 acquires amyloidogenicity via excessive synthesis followed by truncation of its disordered N-terminal region. By identifying a novel in vivo amyloidogenic protein in animals and revealing key mechanistic details of its associated pathology, this study provides valuable insights into the integrated understanding of related proteopathies.
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Affiliation(s)
- Tomoaki Murakami
- Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
| | - Toshisuke Kaku
- Tokyo University of Agriculture and Technology, Koganei-shi, Japan
| | - Kaori Tsukakoshi
- Tokyo University of Agriculture and Technology, Koganei-shi, Japan
| | - Susumu Iwaide
- Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
| | - Yoshiyuki Itoh
- Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
| | - Miki Hisada
- Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
| | | | - Rikako Kubo
- Tokyo University of Agriculture and Technology, Koganei-shi, Japan
| | | | | | - Fuyuki Kametani
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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7
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Fujita K, Takuya H, Tsukakoshi K, Ohno H, Ikebukuro K. The state of water molecules induces changes in the topologies and interactions of G-quadruplex DNA aptamers in hydrated ionic liquid. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120175] [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: 10/31/2022]
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8
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Tu ATT, Hoshi K, Ma Y, Oyama T, Suzuki S, Tsukakoshi K, Nagasawa K, Ikebukuro K, Yamazaki T. Effects of G-Quadruplex Ligands on the Topology, Stability, and Immunostimulatory Properties of G-Quadruplex-Based CpG Oligodeoxynucleotides. ACS Chem Biol 2022; 17:1703-1713. [PMID: 35765965 DOI: 10.1021/acschembio.1c00904] [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 previously reported that the formation of guanine-quadruplex (G4) structures provides phosphodiester oligodeoxynucleotides containing unmethylated cytosine-phosphate-guanine (CpG ODNs) with higher nuclease resistance and cellular uptake, thereby increasing their immunostimulation efficiency through TLR9 activation. CpG ODNs forming G4 structures (G4 CpG ODNs) are thus potential vaccine adjuvants against infectious diseases. However, the G4 structure changes topology depending on the surrounding environment. Recently, G4 ligands, which are small molecules that bind to G4 ODNs with high affinity, were reported to improve the stability of G4. In this study, we propose to increase the stability and function of G4 CpG ODNs using G4 ligands. We show the effects of two G4 ligands, named L2H2-6OTD (L2H2) and L2G2-2M2EG-6OTD (L2G2), on the topology, stability, and immunostimulatory properties of a monomeric hybrid-type G4 CpG ODN containing CpG motifs in the central loop, named GD3. We found that L2H2 helps maintain the hybrid G4 topology of GD3, whereas L2G2 induces parallel G4 formation. Both G4 ligands increase the thermodynamic and nuclease stability of GD3. However, only GD3 associated with L2H2 binds efficiently to TLR9 and evokes a higher immune response from mouse macrophage-like RAW264 cells. GD3 associated with L2G2 does not bind efficiently to TLR9 and elicits lower cytokine production. Our results demonstrate that the potential to enhance immunostimulatory properties depends on the ability of G4 ligands to maintain and stabilize the hybrid G4 of GD3. We anticipate that our findings will facilitate the development of more effective G4 CpG ODN-based vaccine adjuvants against infectious diseases.
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Affiliation(s)
- Anh Thi Tram Tu
- Nanomedicine Group, Research Center for Functional Materials (RCFM), National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.,Division of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan.,Department of Magnetic and Biomedical Materials, Faculty of Materials Science, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh 70000, Viet Nam.,Vietnam National University, Linh Trung Ward, Thu Duc City, Ho Chi Minh 70000, Viet Nam
| | - Kazuaki Hoshi
- Nanomedicine Group, Research Center for Functional Materials (RCFM), National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan
| | - Taiji Oyama
- JASCO Corporation, 2967-5, Ishikawamachi, Hachioji, Tokyo 192-8537, Japan
| | - Satoko Suzuki
- JASCO Corporation, 2967-5, Ishikawamachi, Hachioji, Tokyo 192-8537, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan
| | - Tomohiko Yamazaki
- Nanomedicine Group, Research Center for Functional Materials (RCFM), National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.,Division of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
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9
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Saito T, Shimizu Y, Tsukakoshi K, Abe K, Lee J, Ueno K, Asano R, Jones BV, Yamada T, Nakano T, Tong J, Hishiki A, Hara K, Hashimoto H, Sode K, Toyo'oka T, Todoroki K, Ikebukuro K. Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection. Biosens Bioelectron 2022; 203:114027. [PMID: 35114463 DOI: 10.1016/j.bios.2022.114027] [Citation(s) in RCA: 2] [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: 10/14/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) are successful biomedicines; however, evaluation of their pharmacokinetics and pharmacodynamics demands highly specific discrimination from human immunoglobulin G naturally present in the blood. Here, we developed a novel anti-idiotype aptamer (termed A14#1) with extraordinary specificity against the anti-vascular endothelial growth factor therapeutic mAb, bevacizumab. Structural analysis of the antibody-aptamer complex showed that several bases of A14#1 recognized only the complementarity determining region (CDR) of bevacizumab, thereby contributing to its extraordinary specificity. As the CDR of bevacizumab is predicted to be highly positively charged under mildly acidic conditions and that DNA is negatively charged, the affinity of A14#1 to bevacizumab markedly increased at pH 4.7 (KD = 44 pM) than at pH 7.4 (KD = 12 nM). A14#1-based electrochemical detection method capable of detecting 31 pM of bevacizumab at pH 4.7 was thus developed. A14#1 could be potentially useful for therapeutic drug measurement as a novel ligand of bevacizumab.
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Affiliation(s)
- Taro Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yutaka Shimizu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Kinuko Ueno
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tomohiro Yamada
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Tatsuki Nakano
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Jiaxing Tong
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Asami Hishiki
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA
| | - Toshimasa Toyo'oka
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Kenichiro Todoroki
- Department of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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10
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Fenati RA, Chen Z, Yamagishi Y, Tsukakoshi K, Ikebukuor K, Manian A, Russo SP, Yamazaki T, Ellis AV. Enhancement of DNAzymatic activity using iterative in silico maturation. J Mater Chem B 2022; 10:8960-8969. [DOI: 10.1039/d2tb01638a] [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: 11/11/2022]
Abstract
Enhancement of DNZymatic activity using a combined iterative in silico and in vitro method as a cheaper and more stable alternative to antibodies or enzymes.
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Affiliation(s)
- Renzo A. Fenati
- Flinders Centre for Nanoscale Science and Technology, Flinders University, Sturt Road, Bedford Park, Adelaide, South Australia, 5042, Australia
- School of Chemical and Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia
- ARC Centre of Excellence in Exciton Science, School of Chemistry, Monash University, Clayton, 3800, Australia
| | - Zifei Chen
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville, 3010, Australia
| | - Yasuko Yamagishi
- Department of Biotechnology & Life sciences, Tokyo University of Agriculture and Technology, 2-24-21 Naka-Cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology & Life sciences, Tokyo University of Agriculture and Technology, 2-24-21 Naka-Cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuor
- Department of Biotechnology & Life sciences, Tokyo University of Agriculture and Technology, 2-24-21 Naka-Cho, Koganei, Tokyo, 184-8588, Japan
| | - Anjay Manian
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, 3000, Australia
| | - Salvy P. Russo
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, 3000, Australia
| | - Tomohiko Yamazaki
- Nanomedicine Group, Research Center for Functional Materials, National Institute for Materials Science (NIMS), Tsukuba, Ibaraki, 305-0047, Japan
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0808, Japan
| | - Amanda V. Ellis
- School of Chemical and Biomedical Engineering, Faculty of Engineering and Information Technology, The University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia
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11
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Safitri FA, Tu ATT, Hoshi K, Shobo M, Zhao D, Witarto AB, Sumarsono SH, Giri-Rachman EA, Tsukakoshi K, Ikebukuro K, Yamazaki T. Enhancement of the Immunostimulatory Effect of Phosphodiester CpG Oligodeoxynucleotides by an Antiparallel Guanine-Quadruplex Structural Scaffold. Biomolecules 2021; 11:biom11111617. [PMID: 34827615 PMCID: PMC8615816 DOI: 10.3390/biom11111617] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023] Open
Abstract
Guanine-quadruplex-based CpG oligodeoxynucleotides (G4 CpG ODNs) have been developed as potent immunostimulatory agents with reduced sensitivity to nucleases. We designed new monomeric G4 ODNs with an antiparallel topology using antiparallel type duplex/G4 ODNs as robust scaffolds, and we characterized their topology and effects on cytokine secretion. Based on circular dichroism analysis and quantification of mRNA levels of immunostimulatory cytokines, it was found that monomeric antiparallel G4 CpG ODNs containing two CpG motifs in the first functional loop, named G2.0.0, could maintain antiparallel topology and generate a high level of immunostimulatory cytokines in RAW264 mouse macrophage-like cell lines. We also found that the flanking sequence in the CpG motif altered the immunostimulatory effects. Gc2c.0.0 and Ga2c.0.0 are monomeric antiparallel G4 CpG ODNs with one cytosine in the 3' terminal and one cytosine/adenine in the 5' terminal of CpG motifs that maintained the same resistance to degradation in serum as G2.0.0 and improved interleukin-6 production in RAW264 and bone marrow-derived macrophages. The immunostimulatory activity of antiparallel G4 CpG ODNs is superior to that of linear natural CpG ODNs. These results provide insights for the rational design of highly potent CpG ODNs using antiparallel G4 as a robust scaffold.
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Affiliation(s)
- Fika Ayu Safitri
- Doctoral Program in Biology, School of Life Sciences and Technology, Institut Teknologi Bandung (ITB), Bandung 40132, West Java, Indonesia;
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Anh Thi Tram Tu
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
| | - Kazuaki Hoshi
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Miwako Shobo
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Dandan Zhao
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
| | - Arief Budi Witarto
- Department of Molecular Biology and Biochemistry, Faculty of Medicine, Indonesia Defense University, Bogor 16810, West Java, Indonesia;
| | - Sony Heru Sumarsono
- Physiology, Developmental Biology and Biomedical Sciences Research Group, School of Life Sciences and Technology, ITB, Bandung 40132, West Java, Indonesia; (S.H.S.); (E.A.G.-R.)
| | - Ernawati Arifin Giri-Rachman
- Physiology, Developmental Biology and Biomedical Sciences Research Group, School of Life Sciences and Technology, ITB, Bandung 40132, West Java, Indonesia; (S.H.S.); (E.A.G.-R.)
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan; (K.T.); (K.I.)
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei 184-8588, Japan; (K.T.); (K.I.)
| | - Tomohiko Yamazaki
- Research Center for Functional Materials, National Institute for Materials Science, 1-2-1, Sengen, Tsukuba 305-0047, Japan; (A.T.T.T.); (K.H.); (M.S.); (D.Z.)
- Division of Life Science, Graduate School of Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0808, Japan
- Correspondence: ; Tel.: +81-29-859-2345; Fax: +81-29-859-2449
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Tsukakoshi K, Yamagishi Y, Kanazashi M, Nakama K, Oshikawa D, Savory N, Matsugami A, Hayashi F, Lee J, Saito T, Sode K, Khunathai K, Kuno H, Ikebukuro K. G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Res 2021; 49:6069-6081. [PMID: 34095949 PMCID: PMC8216272 DOI: 10.1093/nar/gkab388] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/07/2023] Open
Abstract
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasuko Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Mana Kanazashi
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kenta Nakama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daiki Oshikawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | | | - Hitoshi Kuno
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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13
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Lee J, Teramoto K, Yokoyama T, Ueno K, Tsukakoshi K, Sode K, Ikebukuro K. Data on G-quadruplex topology, and binding ability of G-quadruplex forming sequences found in the promoter region of biomarker proteins and those relations to the presence of nuclear localization signal in the proteins. Data Brief 2021; 36:107028. [PMID: 33948456 PMCID: PMC8080463 DOI: 10.1016/j.dib.2021.107028] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 11/24/2022] Open
Abstract
Aptamer is a nucleic acid ligand which specifically binds to its target molecule. Previously, we have designed an identification method of aptamer called "G-quadruplex (G4) promoter-derived aptamer selection (G4PAS)" [1]. In G4PAS procedure, putative G4 forming sequences (PQS) were explored in a promoter region of a target protein in human gene through computational analysis, and evaluated binding ability towards the gene product encoded in the downstream of the promoter. We investigated the topology of the obtained PQSs by circular dichroism measurement, as well as their binding ability against its target protein by surface plasmon resonance measurement and gel-shift assay. Additionally, the presence of nuclear localization signal in the target protein was predicted in silico. This data set summarized all the PQS sequences, their biochemical characteristics, and the presence of nuclear localization signal to address the possibility of binding of these PQS region to the target proteins in vivo. Those data should contribute to increase the success rate of G4PAS. Moreover, considering the G4 motifs in genomic DNA are suggested to be involved in vivo gene regulation [2], [3], this data set is also potentially beneficial for the cell biology field.
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Affiliation(s)
- Jinhee Lee
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Kentaro Teramoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tomomi Yokoyama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kinuko Ueno
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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14
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Shono C, Ariyanti D, Abe K, Sakai Y, Sakamoto I, Tsukakoshi K, Sode K, Ikebukuro K. A Green Light-Regulated T7 RNA Polymerase Gene Expression System for Cyanobacteria. Mar Biotechnol (NY) 2021; 23:31-38. [PMID: 32979137 DOI: 10.1007/s10126-020-09997-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
In this study, we developed a green light-regulated T7 RNA polymerase expression system (T7 RNAP system), to provide a novel and versatile high-expression system for cyanobacteria without using any chemical inducer, realizing high expression levels comparable with previously reported for recombinant gene expression in cyanobacteria. The T7 RNAP system was constructed and introduced into Synechocystis sp. PCC6803. T7 RNAP was inserted downstream of the cpcG2 promoter, which is recognized and activated by the CcaS/CcaR two-component green-light-sensing system, to compose a vector plasmid, pKT-CS01, to achieve the induction of T7 RNAP expression only under green light illumination, with repression under red light illumination. The reporter gene, superfolder green fluorescent protein (sfGFP), was inserted downstream of the T7 promoter. Transcriptional analyses revealed that T7 RNAP was induced under green light but repressed under red light. Expression of the sfGFP protein derived from pKT-CS01 was observed under green light illumination and was approximately 10-fold higher than that in the control transformant, which expressed sfGFP directly under the cpcG2 promoter, which is directly regulated by CcaS/CcaR, under green light illumination. Comparison with the strong promoter expression systems Pcpc560 and PtrcΔlacO revealed that the expression of sfGFP by the T7 RNAP system was comparable with the levels obtained with strong promoters. These results demonstrated that the green light-regulated T7 RNAP gene expression system will be a versatile tool for future technological platform to regulate gene expression in cyanobacterial bioprocesses.
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Affiliation(s)
- Chika Shono
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Dwi Ariyanti
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
- Faculty of Biotechnology, Sumbawa University of Technology, Olat Maras, Moyo Hulu, Sumbawa, West Nusa Tenggara, 84371, Indonesia
| | - Koichi Abe
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Yuta Sakai
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Ippei Sakamoto
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan.
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan.
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Nishio M, Tsukakoshi K, Ikebukuro K. G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing. Biosens Bioelectron 2021; 178:113030. [PMID: 33524709 DOI: 10.1016/j.bios.2021.113030] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 12/20/2022]
Abstract
G-quadruplex (G4) is a non-canonical structure that is formed in G-rich sequences of nucleic acids. G4s play important roles in vivo, such as telomere maintenance, transcription, and DNA replication. There are three typical topologies of G4: parallel, anti-parallel, and hybrid. In general, metal cations, such as potassium and sodium, stabilize G4s through coordination in the G-quartet. While G4s have some functions in vivo, there are many reports of developed applications that use G4s. As various conformations of G4s could form from one sequence depending on varying conditions, many researchers have developed G4-based sensors. Furthermore, G4 is a great scaffold of aptamers since many aptamers folded into G4s have also been reported. However, there are some challenges about its practical use due to the difference between practical sample conditions and experimental ones. G4 conformations are dramatically altered by the surrounding conditions, such as metal cations, pH, and crowding. Many studies have been conducted to characterize G4 conformations under various conditions, not only to use G4s in practical applications but also to reveal its function in vivo. In this review, we summarize recent studies that have investigated the effects of surrounding conditions (e.g., metal cations, pH, and crowding) on G4 conformations and the application of G4s mainly in biosensor fields, and in others.
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Affiliation(s)
- Maui Nishio
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Lee J, Tatsumi A, Tsukakoshi K, Wilson ED, Abe K, Sode K, Ikebukuro K. Application of a Glucose Dehydrogenase-Fused with Zinc Finger Protein to Label DNA Aptamers for the Electrochemical Detection of VEGF. Sensors (Basel) 2020; 20:s20143878. [PMID: 32664558 PMCID: PMC7411789 DOI: 10.3390/s20143878] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022]
Abstract
Aptamer-based electrochemical sensors have gained attention in the context of developing a diagnostic biomarker detection method because of their rapid response, miniaturization ability, stability, and design flexibility. In such detection systems, enzymes are often used as labels to amplify the electrochemical signal. We have focused on glucose dehydrogenase (GDH) as a labeling enzyme for electrochemical detection owing to its high enzymatic activity, availability, and well-established electrochemical principle and platform. However, it is difficult and laborious to obtain one to one labeling of a GDH-aptamer complex with conventional chemical conjugation methods. In this study, we used GDH that was genetically fused to a DNA binding protein, i.e., zinc finger protein (ZF). Fused GDH can be attached to an aptamer spontaneously and site specifically in a buffer by exploiting the sequence-specific binding ability of ZF. Using such a fusion protein, we labeled a vascular endothelial growth factor (VEGF)-binding aptamer with GDH and detected the target electrochemically. As a result, upon the addition of glucose, the GDH labeled on the aptamer generated an amperometric signal, and the current response increased dependent on the VEGF concentration. Eventually, the developed electrochemical sensor proved to detect VEGF levels as low as 105 pM, thereby successfully demonstrating the concept of using ZF-fused GDH to enzymatically label aptamers.
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Affiliation(s)
- Jinhee Lee
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; (J.L.); (E.D.W.); (K.S.)
| | - Atsuro Tatsumi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
| | - Ellie D. Wilson
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; (J.L.); (E.D.W.); (K.S.)
| | - Koichi Abe
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; (J.L.); (E.D.W.); (K.S.)
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; (A.T.); (K.T.); (K.A.)
- Correspondence: ; Tel.: +81-42-388-7030
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17
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Tanifuji R, Tsukakoshi K, Ikebukuro K, Oikawa H, Oguri H. Generation of C5-desoxy analogs of tetrahydroisoquinoline alkaloids exhibiting potent DNA alkylating ability. Bioorg Med Chem Lett 2019; 29:1807-1811. [DOI: 10.1016/j.bmcl.2019.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/23/2019] [Accepted: 05/07/2019] [Indexed: 11/25/2022]
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18
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Hoshi K, Yamazaki T, Sugiyama Y, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K. G-Quadruplex Structure Improves the Immunostimulatory Effects of CpG Oligonucleotides. Nucleic Acid Ther 2019; 29:224-229. [PMID: 30835633 DOI: 10.1089/nat.2018.0761] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Single-strand oligodeoxynucleotides (ODNs) containing unmethylated cytosine-phosphate-guanine (CpG) are recognized by the toll-like receptor 9, a component of the innate immunity. Therefore, they could act as immunotherapeutic agents. Chemically modified CpG ODNs containing a phosphorothioate backbone instead of phosphodiester (PD) were developed as immunotherapeutic agents resistant to nuclease degradation. However, they cause adverse side effects, and so there is a necessity to generate novel CpG ODNs. In the present study, we designed a nuclease-resistant nonmodified CpG ODN that forms G-quadruplex structures. G-quadruplex formation in CpG ODNs increased nuclease resistance and cellular uptake. The CpG ODNs designed in this study induced interleukin-6 production in a human B lymphocyte cell line and human peripheral blood mononuclear cells. These results indicate that G-quadruplex formation can be used to increase the immunostimulatory activity of CpG ODNs having a natural PD backbone.
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Affiliation(s)
- Kazuaki Hoshi
- 1Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tomohiko Yamazaki
- 2Research Center for Functional Materials, National Institute for Materials Science (NIMS), Tsukuba, Japan
| | - Yuuki Sugiyama
- 1Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kaori Tsukakoshi
- 1Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Wakako Tsugawa
- 1Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Koji Sode
- 3Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina
| | - Kazunori Ikebukuro
- 1Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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19
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Yamada T, Saito T, Shimizu Y, Tsukakoshi K, Hayashi H, Mizuno H, Tsuji D, Yamamoto K, Itoh K, Toyo'oka T, Ikebukuro K, Todoroki K. Anti-Idiotype DNA Aptamer Affinity Purification⁻High-Temperature Reversed-Phase Liquid Chromatography: A Simple, Accurate, and Selective Bioanalysis of Bevacizumab. Molecules 2019; 24:molecules24050857. [PMID: 30823418 PMCID: PMC6429324 DOI: 10.3390/molecules24050857] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/18/2022] Open
Abstract
This study presents a simple, accurate, and selective bioanalytical method of bevacizumab detection from plasma samples based on aptamer affinity purification–high-temperature reversed-phased liquid chromatography (HT-RPLC) with fluorescence detection. Bevacizumab in plasma samples was purified using magnetic beads immobilized with an anti-idiotype DNA aptamer for bevacizumab. The purified bevacizumab was separated with HT-RPLC and detected with its native fluorescence. Using aptamer affinity beads, bevacizumab was selectively purified and detected as a single peak in the chromatogram. HT-RPLC achieved good separation for bevacizumab with a sharp peak within 10 min. The calibration curves of the two monoclonal antibodies ranged from 1 to 50 μg/mL and showed good correlation coefficients (r2 > 0.999). The limit of detection (LOD) and lower limit of quantification (LLOQ) values for bevacizumab were 0.15 and 0.51 μg/mL, respectively. The proposed method was successfully applied to the bioanalysis of the plasma samples obtained from the patients with lung cancer and may be extended to plan optimal therapeutic programs and for the evaluation of biological equivalencies in the development of biosimilars.
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Affiliation(s)
- Tomohiro Yamada
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 4228526, Japan.
| | - Taro Saito
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan.
| | - Yutaka Shimizu
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan.
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan.
| | - Hideki Hayashi
- Laboratory of Pharmacy Practice and Social Science, Gifu Pharmaceutical University, Gifu 501-1196, Japan.
| | - Hajime Mizuno
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 4228526, Japan.
| | - Daiki Tsuji
- Laboratory of Clinical Pharmacology and Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 4228526, Japan.
| | - Keisuke Yamamoto
- Department of Pharmacy, Seirei Hamamatsu General Hospital, Hamamatsu 4300906, Japan.
| | - Kunihiko Itoh
- Laboratory of Clinical Pharmacology and Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 4228526, Japan.
| | - Toshimasa Toyo'oka
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 4228526, Japan.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan.
| | - Kenichiro Todoroki
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 4228526, Japan.
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20
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Yamada T, Saito T, Hill Y, Shimizu Y, Tsukakoshi K, Mizuno H, Hayashi H, Ikebukuro K, Toyo'oka T, Todoroki K. High-Throughput Bioanalysis of Bevacizumab in Human Plasma Based on Enzyme-Linked Aptamer Assay Using Anti-Idiotype DNA Aptamer. Anal Chem 2019; 91:3125-3130. [PMID: 30667211 DOI: 10.1021/acs.analchem.8b05725] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We propose a highly selective, sensitive, accurate, and high-throughput bioanalysis method for bevacizumab utilizing an anti-idiotype DNA aptamer. With this method, bevacizumab in a plasma sample was reacted in a 96-well plate immobilized with the aptamer and further reacted with a protein A-HRP conjugate. The resulting HRP activity was colorimetrically detected using a microplate reader. The calibration curve of bevacizumab ranged from 0.05 to 5.0 μg/mL, and showed a good correlation coefficient ( r2 = 1.000). The limit of detection was 2.09 ng/mL. We also demonstrated both the possibility of highly sensitive detection using luminol chemiluminescence and the repeated use of affinity plates. The proposed method is applicable for planning optimal therapeutic programs and for an evaluation of the biological equivalencies in the development of biosimilars.
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Affiliation(s)
- Tomohiro Yamada
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Taro Saito
- Department of Biotechnology and Life Science, Graduate School of Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
| | - Yoshia Hill
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Yutaka Shimizu
- Department of Biotechnology and Life Science, Graduate School of Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
| | - Hajime Mizuno
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Hideki Hayashi
- Laboratory of Pharmacy Practice and Social Science , Gifu Pharmaceutical University , Daigaku-nishi 1-25-4 , Gifu 501-1196 , Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering , Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho , Koganei , Tokyo 184-8588 , Japan
| | - Toshimasa Toyo'oka
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
| | - Kenichiro Todoroki
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences , University of Shizuoka , 52-1 Yada , Suruga-ku, Shizuoka 422-8526 , Japan
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21
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Tsukakoshi K, Yoshida W, Kobayashi M, Kobayashi N, Kim J, Kaku T, Iguchi T, Nagasawa K, Asano R, Ikebukuro K, Sode K. Esterification of PQQ Enhances Blood-Brain Barrier Permeability and Inhibitory Activity against Amyloidogenic Protein Fibril Formation. ACS Chem Neurosci 2018; 9:2898-2903. [PMID: 30074759 DOI: 10.1021/acschemneuro.8b00355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 02/04/2023] Open
Abstract
Several neurodegenerative diseases have a common pathophysiology where selective damage to neurons results from the accumulation of amyloid oligomer proteins formed via fibrilization. Considering that the formation of amyloid oligomers leads to cytotoxicity, the development of chemical compounds that are able to effectively cross the blood-brain barrier (BBB) and inhibit this conversion to oligomers and/or fibrils is essential for neurodegenerative disease therapy. We previously reported that pyrroloquinoline quinone (PQQ) prevented aggregation and fibrillation of α-synuclein, amyloid β1-42 (Aβ1-42), and mouse prion protein. To develop a novel drug against neurodegenerative diseases based on PQQ, it is necessary to improve the insufficient BBB permeability of PQQ. Here, we show that an esterified compound of PQQ, PQQ-trimethylester (PQQ-TME), has twice the BBB permeability than PQQ in vitro. Moreover, PQQ-TME exhibited greater inhibitory activity against fibrillation of α-synuclein, Aβ1-42, and prion protein. These results indicated that esterification of PQQ could be a useful approach in developing a novel PQQ-based amyloid inhibitor.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan
| | - Masaki Kobayashi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Natsuki Kobayashi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Jihoon Kim
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Toshisuke Kaku
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Toshitsugu Iguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
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22
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Tsukakoshi K, Saito S, Yoshida W, Goto S, Ikebukuro K. CpG Methylation Changes G-Quadruplex Structures Derived from Gene Promoters and Interaction with VEGF and SP1. Molecules 2018; 23:molecules23040944. [PMID: 29670067 PMCID: PMC6017926 DOI: 10.3390/molecules23040944] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/13/2018] [Accepted: 04/15/2018] [Indexed: 12/14/2022] Open
Abstract
G-quadruplex (G4) is a DNA/RNA conformation that consists of two or more G-tetrads resulting from four-guanine bases connected by Hoogsteen-type hydrogen bonds, which is often found in the telomeres of chromatin, as well as in the promoter regions of genes. The function of G4 in the genomic DNA is being elucidated and some G4-protein interactions have been reported; these are believed to play a role in vital cellular functions. In this study, we focused on CpG methylation, a well-known epigenetic modification of the genomic DNA, especially found in the promoter regions. Although many G4-forming sequences within the genomic DNA harbor CpG sites, the relationship between CpG methylation and the binding properties of associated proteins remains unclear. We demonstrated that the binding ability of vascular endothelial growth factor (VEGF) G4 DNA to VEGF165 protein was significantly decreased by CpG methylation. We identified the binding activity of G4 DNA oligonucleotides derived from gene promoter regions to SP1, a transcription factor that interacts with a G4-forming DNA and is also altered by CpG methylation. The effect of methylation on binding affinity was accompanied by changes in G4 structure and/or topology. Therefore, this study suggested that CpG methylation might be involved in protein binding to G4-forming DNA segments for purposes of transcriptional regulation.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Shiori Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Shinichi Goto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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23
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Sakamoto I, Abe K, Kawai S, Tsukakoshi K, Sakai Y, Sode K, Ikebukuro K. Improving the induction fold of riboregulators for cyanobacteria. RNA Biol 2018; 15:353-358. [PMID: 29303421 DOI: 10.1080/15476286.2017.1422470] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Cyanobacteria are ideal cellular factories for biochemical production because of their ability to fix CO2 by photosynthesis and convert this molecule into biochemicals. Previously, we engineered a riboregulator that enables post-transcriptional gene regulation in the cyanobacterium Synechocystis sp. PCC 6803. Here, we improved the riboregulator by designing two RNA species, taRNA and crRNA, to enhance its induction fold. We inserted nucleotides into the crRNA loop to enhance intermolecular hybridization and successfully improved its induction fold. The engineered riboregulator exhibited a higher induction fold than the previously engineered riboregulator in both Escherichia coli and Synechocystis sp. PCC 6803. This improved riboregulator can be used to control gene expression over a wide dynamic range in cyanobacteria.
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Affiliation(s)
- Ippei Sakamoto
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
| | - Koichi Abe
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
| | - Sumiya Kawai
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
| | - Kaori Tsukakoshi
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
| | - Yuta Sakai
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
| | - Koji Sode
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
| | - Kazunori Ikebukuro
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Tokyo , Japan
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24
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Ueno K, Sakai Y, Shono C, Sakamoto I, Tsukakoshi K, Hihara Y, Sode K, Ikebukuro K. Applying a riboregulator as a new chromosomal gene regulation tool for higher glycogen production in Synechocystis sp. PCC 6803. Appl Microbiol Biotechnol 2017; 101:8465-8474. [PMID: 29038975 DOI: 10.1007/s00253-017-8570-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 06/04/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
Cyanobacteria are one of the most attractive hosts for biofuel production; however, genetic approaches to regulate specific chromosomal genes in cyanobacteria remain limited. With the aim of developing a novel method to regulate chromosomal gene expression in cyanobacteria, we focused on riboregulatory technology. Riboregulators are composed of two RNA fragments whose interaction leads to target gene regulation with high specificity. In this study, we inserted a riboregulator sequence upstream of the chromosomal gene encoding AbrB-like transcriptional regulator, cyAbrB2, to investigate the utility of this tool. The inserted riboregulator was able to regulate cyabrB2 gene expression, with a high ON-OFF ratio up to approximately 50-fold. The transcription levels of several genes for which cyAbrB2 acts as a transcriptional upregulator were also decreased. Further, the cyAbrB2 expression-repressed mutant showed high glycogen accumulation, equivalent to that in the cyabrB2 deletion mutant (ΔcyabrB2). Phenotypic similarities between the cyabrB2 expression-repressed mutant and the ΔcyabrB2 mutant suggest that the riboregulator can potentially be used as a new chromosomal gene regulation tool in cyanobacteria.
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Affiliation(s)
- Kinuko Ueno
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yuta Sakai
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Chika Shono
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Ippei Sakamoto
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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25
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Yokoyama T, Tsukakoshi K, Yoshida W, Saito T, Teramoto K, Savory N, Abe K, Ikebukuro K. Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation. Biotechnol Bioeng 2017. [PMID: 28627727 DOI: 10.1002/bit.26354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe the selection of aptamers based on bioinformatics-based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR-amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer-screening method, G4 promoter-derived aptamer selection (G4PAS), and an aptamer-improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45-fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196-2203. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tomomi Yokoyama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wataru Yoshida
- School of Biotechnology and Bioscience, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kentaro Teramoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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26
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Nishio M, Matsumoto D, Kato Y, Abe K, Lee J, Tsukakoshi K, Yamagishi A, Nakamura C, Ikebukuro K. DNA aptamers against FokI nuclease domain for genome editing applications. Biosens Bioelectron 2016; 93:26-31. [PMID: 27899266 DOI: 10.1016/j.bios.2016.11.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 01/08/2023]
Abstract
Genome editing with site-specific nucleases (SSNs) can modify only the target gene and may be effective for gene therapy. The main limitation of genome editing for clinical use is off-target effects; excess SSNs in the cells and their longevity can contribute to off-target effects. Therefore, a controlled delivery system for SSNs is necessary. FokI nuclease domain (FokI) is a common DNA cleavage domain in zinc finger nuclease (ZFN) and transcription activator-like effector nuclease. Previously, we reported a zinc finger protein delivery system that combined aptamer-fused, double-strand oligonucleotides and nanoneedles. Here, we report the development of DNA aptamers that bind to the target molecules, with high affinity and specificity to the FokI. DNA aptamers were selected in six rounds of systematic evolution of ligands by exponential enrichment. Aptamers F6#8 and #71, which showed high binding affinity to FokI (Kd=82nM, 74nM each), showed resistance to nuclease activity itself and did not inhibit nuclease activity. We immobilized the ZFN-fused GFP to nanoneedles through these aptamers and inserted the nanoneedles into HEK293 cells. We observed the release of ZFN-fused GFP from the nanoneedles in the presence of cells. Therefore, these aptamers are useful for genome editing applications such as controlled delivery of SSNs.
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Affiliation(s)
- Maui Nishio
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daisuke Matsumoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Jinhee Lee
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ayana Yamagishi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Chikashi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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27
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Tsukakoshi K, Ikuta Y, Abe K, Yoshida W, Iida K, Ma Y, Nagasawa K, Sode K, Ikebukuro K. Structural regulation by a G-quadruplex ligand increases binding abilities of G-quadruplex-forming aptamers. Chem Commun (Camb) 2016; 52:12646-12649. [DOI: 10.1039/c6cc07552e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By the binding of a G4 ligand to G4-forming aptamers, their conformations became suitable for binding to the target and their binding ability increased.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Yuri Ikuta
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Wataru Yoshida
- School of Biotechnology and Bioscience
- Tokyo University of Technology
- Tokyo 192-0982
- Japan
| | - Keisuke Iida
- Graduate School of Science and Engineering
- Saitama University
- Sakura-ku
- Japan
| | - Yue Ma
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Koji Sode
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
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28
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Fukaya T, Abe K, Savory N, Tsukakoshi K, Yoshida W, Ferri S, Sode K, Ikebukuro K. Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy. J Biotechnol 2015; 212:99-105. [PMID: 26302839 DOI: 10.1016/j.jbiotec.2015.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/25/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
Abstract
Aptamers are mainly selected by in vitro selection using random nucleic acid libraries. These aptamers have often shown insufficient affinity for biomedical applications. We improved DNA aptamer binding affinity for vascular endothelial growth factor (VEGF) through in silico maturation (ISM) and aptamer multimerization. ISM is one of a number of evolutionary approaches and aptamer multimerization is one of several semi-rational strategies to improve function. We first reselected VEGF-binding aptamers using a partially randomized DNA library and identified two aptamers with higher binding ability than that of a known aptamer. We conducted ISM using the re-selected aptamers to optimize the key loop sequences created by a three-way junction structure. After five ISM rounds, we identified aptamer 2G19 [dissociation constant (Kd), 52 nM] as a local optimum of the defined search space. We characterized the aptamer and found that a specific stem-loop structure was involved in aptamer VEGF recognition. To further improve its affinity for VEGF, we multimerized 2G19 or its stem-loop structure. The designed SL5-trivalent aptamer (Kd, 0.37 nM) with three binding motifs significantly increased binding affinity, representing a 500-fold improvement from systematic evolution of ligands by exponential enrichment-selected aptamers.
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Affiliation(s)
- Takahiro Fukaya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, Japan
| | - Stefano Ferri
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
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Tsukakoshi K, Saito T, Saido T. P3‐125: SCREENING OF PLASMA PROTEIN BIOMARKER CANDIDATES FOR ALZHEIMER'S DISEASE USING A SINGLE APP LOCUS KNOCKIN MICE. Alzheimers Dement 2014. [DOI: 10.1016/j.jalz.2014.05.1214] [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: 10/24/2022]
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Savory N, Takahashi Y, Tsukakoshi K, Hasegawa H, Takase M, Abe K, Yoshida W, Ferri S, Kumazawa S, Sode K, Ikebukuro K. Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development. Biotechnol Bioeng 2013; 111:454-61. [PMID: 24018905 DOI: 10.1002/bit.25111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/27/2013] [Accepted: 09/03/2013] [Indexed: 01/23/2023]
Abstract
In silico evolution with an in vitro system can facilitate the development of functional aptamers with high specificity and affinity. Although a general technique known as systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method for aptamer selection, it sometimes fails to identify aptamers with sufficient binding properties. We have previously developed in silico maturation (ISM) to improve functions of aptamers based on genetic algorithms. ISM represents an intelligent exploitation of a random search within a defined sequence space to optimize aptamer sequences and improve their function of interest. Here we demonstrated a successful application of ISM of aptamers to simultaneously improve specificity and affinity for Streptococcus mutans with discovery of a core sequence, which was required to form a polymerized guanine quadruplex structure for target binding. We applied ISM to aptamers selected by whole-cell SELEX and identified an aptamer with up to 16-fold improvement in affinity compared to its parent aptamers, and specificity was increased to show 12-fold more binding to S. mutans than to Lactobacillus acidophilus. Furthermore, we demonstrated a specific flow-through detection of S. mutans at a concentration range of 1 × 10(5) -10(8) CFU/mL using the evolved aptamer immobilized on gold colloids.
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Affiliation(s)
- Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
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Savory N, Lednor D, Tsukakoshi K, Abe K, Yoshida W, Ferri S, Jones BV, Ikebukuro K. In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis. Biotechnol Bioeng 2013; 110:2573-80. [PMID: 23568752 DOI: 10.1002/bit.24922] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 01/04/2013] [Revised: 02/27/2013] [Accepted: 03/29/2013] [Indexed: 01/23/2023]
Abstract
Proteus mirabilis is a prominent cause of catheter-associated urinary tract infections (CAUTIs) among patients undergoing long-term bladder catheterization. There are currently no effective means of preventing P. mirabilis infections, and strategies for prophylaxis and rapid early diagnosis are urgently required. Aptamers offer significant potential for development of countermeasures against P. mirabilis CAUTI and are an ideal class of molecules for the development of diagnostics and therapeutics. Here we demonstrate the application of Cell-SELEX to identify DNA aptamers that show high affinity for P. mirabilis. While the aptamers identified displayed high affinity for P. mirabilis cells in dot blotting assays, they also bound to other uropathogenic bacteria. To improve aptamer specificity for P. mirabilis, an in silico maturation (ISM) approach was employed. Two cycles of ISM allowed the identification of an aptamer showing 36% higher specificity, evaluated as a ratio of binding signal for P. mirabilis to that for Escherichia coli (also a cause of CAUTI and the most common urinary tract pathogen). Aptamers that specifically recognize P. mirabilis would have diagnostic and therapeutic values and constitute useful tools for studying membrane-associated proteins in this organism.
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Affiliation(s)
- Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
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Tsukakoshi K, Abe K, Sode K, Ikebukuro K. Selection of DNA aptamers that recognize α-synuclein oligomers using a competitive screening method. Anal Chem 2012; 84:5542-7. [PMID: 22697251 DOI: 10.1021/ac300330g] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [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
α-Synuclein (α-syn) oligomers are considered major molecules responsible for the onset of Parkinson's disease and dementia with Lewy bodies. α-Syn oligomers thus serve as an important target for the development of drugs and diagnostic tests for neurodegenerative diseases. In this paper we report on the identification of DNA aptamers that bind to soluble α-syn oligomers. A competitive screening method based on aptamer blotting was used for the selection of α-syn oligomer-specific aptamers. This approach resulted in the identification of eight aptamers that specifically bind to α-syn oligomers among α-syn monomers, oligomers, and fibrils. Interestingly, the aptamers also bound to amyloid β oligomers, which are strongly associated with the development of Alzheimer's disease. The results of this study support the hypothesis that amyloid oligomers share a common structure. Oligomer-binding aptamers may serve as powerful analytical tools for the design and development of drugs and diagnostic tests for neurodegenerative diseases.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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Tsukakoshi K, Abe K, Sode K, Ikebukuro K. P2‐076: Development of DNA aptamers that bind to amyloid oligomers. Alzheimers Dement 2011. [DOI: 10.1016/j.jalz.2011.05.966] [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: 11/29/2022]
Affiliation(s)
| | - Koichi Abe
- Tokyo University of Agriculture and TechnologyTokyoJapan
| | - Koji Sode
- Tokyo University of Agriculture and TechnologyTokyoJapan
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Tsukakoshi K, Ogasawara D, Takahashi E, Katayama R, Ikebukuro K. Non-label homogeneous protein detection based on laser interferometric photo-thermal displacement measurement using aptamers. Biotechnol J 2011; 6:101-6. [PMID: 21086453 DOI: 10.1002/biot.201000158] [Citation(s) in RCA: 3] [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: 11/09/2022]
Abstract
Photo-thermal displacement measurement by laser interferometry involves the measurement of temperature change caused by illumination of the sample. To develop a system of detecting unlabeled homogeneous proteins based on laser interferometric measurement of photo-thermal displacement, we studied the interaction between aptamers and their target molecules by using thrombin and the thrombin aptamer as a model target and ligand, respectively. Because of the energy consumed by aptamer-thrombin interactions, the signals obtained from solutions containing aptamer-thrombin mixtures varied depending on the thrombin concentration. We propose that this method involving the use of aptamers and photo-thermal displacement measurement will provide a biomolecular detection system for rapid diagnosis.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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Tsukakoshi K, Harada R, Sode K, Ikebukuro K. Screening of DNA aptamer which binds to alpha-synuclein. Biotechnol Lett 2010; 32:643-8. [PMID: 20111982 DOI: 10.1007/s10529-010-0200-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 12/18/2009] [Accepted: 12/21/2009] [Indexed: 11/25/2022]
Abstract
Alpha-synuclein is a native, unfolded protein that causes several neurodegenerative diseases such as dementia with Lewy bodies and Parkinson's disease. We have now identified the first DNA aptamers against alpha-synuclein using native PAGE applied to the SELEX method. We call this aptamer "M5-15"; it is the alpha-synuclein-bound aptamer and was isolated after four cycles of screening. M5-15 is composed of three stem-loop structures that may play an important role in the binding to alpha-synuclein. Moreover, M5-15 specifically binds to the alpha-synuclein monomer and oligomer. We expect that this aptamer will become a useful tool in alpha-synuclein analysis and diagnosis.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
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