1
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Ouchi K, Haraga T, Hirose K, Kurosawa Y, Sato Y, Shibukawa M, Saito S. Determination of 90Sr in highly radioactive aqueous samples via conversion to a kinetically stable 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid complex followed by concentration-separation-fractionation based on capillary electrophoresis-liquid scintillation. Anal Chim Acta 2024; 1298:342399. [PMID: 38462347 DOI: 10.1016/j.aca.2024.342399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND The Fukushima Daiichi Nuclear Power Plant accident (2011) released large amounts of radioactive substances into the environment and generated highly radioactive debris. Post-accident countermeasures are currently in the phase of fuel debris removal, which requires the analysis of radioactive contaminants in the environment and fuel. The spectra of solely β-emitting nuclides, such as 90Sr, overlap; thus, an effective method for nuclide separation is desired. Since conventional methods for high-dose sample analysis pose substantial exposure risks and generate large amounts of secondary radioactive waste, faster procedures allowing for decreased radiation emission are highly desirable. RESULTS In this study, we developed a 90Sr2+ quantitation technique based on liquid scintillation counting (LSC)-coupled capillary transient isotachophoresis (ctITP), along with two-point detection and relying on the rapid concentration, separation, and fractionation of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)-complexed 90Sr2+ in a single run. The applicability of our method for the analysis of real-world samples was verified by conducting addition-recovery experiments using a seawater reference material and radioactive liquid waste obtained from the radioactive waste treatment facility at the Japan Atomic Energy Agency. The recovery determined by LSC was 95-113%, indicating successful quantitative analysis. 90Sr recovery was determined to be 90.1% from a contaminated water sample obtained from the Fukushima Daiichi Nuclear Power Plant, which was analyzed using the standard addition of 90Sr. The sensitivity (detection limit = 0.016 Bq) of the proposed method on a radioactivity basis was equal to or higher than that of the conventional method using ion exchange-LSC (0.012-0.07 Bq). SIGNIFICANCE AND NOVELTY Our method allows for the handling of high-dose radioactive samples at the microliter level and is substantially faster than conventional ion exchange protocols, whereas ctITP has not been used for practical applications due to inaccurate collection and lack of a suitable chemical system. The concentration-separation-fractionation protocol in ctITP is successful due to the existence of a rare inert Sr2+ complex and precise fractionation. This study establishes a pathway toward safer and more practical analysis of radionuclides.
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Affiliation(s)
- Kazuki Ouchi
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki, 319-1195, Japan; Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Tomoko Haraga
- Department of Decommissioning and Waste Management, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki, 319-1195, Japan.
| | - Kazuki Hirose
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Yuika Kurosawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Yoshiyuki Sato
- Department of Decommissioning and Waste Management, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki, 319-1195, Japan
| | - Masami Shibukawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
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2
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Hui J, Majikes JM, Riley KR. Analysis of DNA Origami Nanostructures Using Capillary Electrophoresis. Anal Chem 2023; 95:18783-18792. [PMID: 38088564 PMCID: PMC10753524 DOI: 10.1021/acs.analchem.3c03641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/27/2023]
Abstract
DNA origami nanostructures are engineered nanomaterials (ENMs) that possess significant customizability, biocompatibility, and tunable structural and functional properties, making them potentially useful materials in fields, such as medicine, biocomputing, biomedical engineering, and measurement science. Despite the potential of DNA origami as a functional nanomaterial, a major barrier to its applicability is the difficulty associated with obtaining pure, well-folded structures. Therefore, rapid methods of analysis to ensure purity are needed to support the rapid development of this class of nanomaterials. Here, we present the development of capillary electrophoresis (CE) as an analytical tool for DNA origami. CE was investigated under both capillary zone electrophoresis (CZE) and capillary transient isotachophoresis (ctITP) modes. Optimization of both systems yielded baseline resolved separations of folded DNA origami nanostructures from excess staple strands. The ctITP separation mode demonstrated superior performance in terms of peak resolution (Rs = 2.05 ± 0.3), peak efficiency (N = 12,200 ± 230), and peak symmetry (As = 1.29 ± 0.032). The SYBR family dyes (Gold, Green I, and Green II) were investigated as highly efficient, noncovalent fluorophores for on-column labeling of DNA origami and detection using laser-induced fluorescence. Finally, ctITP analysis conditions were also applied to DNA origami nanostructures with different shapes and for the differentiation of DNA origami aggregates.
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Affiliation(s)
- Janan Hui
- Department
of Chemistry and Biochemistry, Swarthmore
College, Swarthmore, Pennsylvania 19081, United States
| | - Jacob M. Majikes
- Physical
Measurement Laboratory, National Institute
of Standards and Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Kathryn R. Riley
- Department
of Chemistry and Biochemistry, Swarthmore
College, Swarthmore, Pennsylvania 19081, United States
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3
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Takao J, Nagai R, Endo T, Hisamoto H, Sueyoshi K. Aptamer Selection Based on Microscale Electrophoretic Filtration Using a Hydrogel-Plugged Capillary Device. Molecules 2022; 27:molecules27185818. [PMID: 36144553 PMCID: PMC9505737 DOI: 10.3390/molecules27185818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
This study reports a novel aptamer selection method based on microscale electrophoretic filtration. Aptamers are versatile materials that recognize specific targets and are attractive for their applications in biosensors, diagnosis, and therapy. However, their practical applications remain scarce due to issues with conventional selection methods, such as complicated operations, low-efficiency separation, and expensive apparatus. To overcome these drawbacks, a selection method based on microscale electrophoretic filtration using a capillary partially filled with hydrogel was developed. The electrophoretic filtration of model target proteins (immunoglobulin E (IgE)) using hydrogel, the electrokinetic injection of DNAs to interact with the trapped proteins, the elimination of DNAs with weak interactions, and the selective acquisition of aptamer candidates with strong interactions were successfully demonstrated, revealing the validity of the proposed concept. Two aptamer candidates for IgE were obtained after three selection cycles, and their affinity for the target was confirmed to be less than 1 nM based on their dissociation constant (KD) values. Therefore, the proposed method allows for the selection of aptamers with simple operations, highly effective separation based on electrophoresis and filtration, and a relatively cheap apparatus with disposable devices.
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Affiliation(s)
- Junku Takao
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Reina Nagai
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
- Correspondence:
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4
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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5
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Xiao X, Li H, Zhao L, Zhang Y, Liu Z. Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications. Biomed Pharmacother 2021; 143:112232. [PMID: 34649356 DOI: 10.1016/j.biopha.2021.112232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/04/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.
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Affiliation(s)
- Xueran Xiao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hui Li
- Department of Urology, Peking University International Hospital, Beijing 102206, China
| | - Lijian Zhao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yanfen Zhang
- Technology Transfer Center, Hebei University, Baoding 071002, China.
| | - Zhongcheng Liu
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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6
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Saito S, Sakamoto T, Tanaka N, Watanabe R, Kamimura T, Ota K, Riley KR, Yoshimoto K, Tasaki-Handa Y, Shibukawa M. Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers. Chemistry 2021; 27:10058-10067. [PMID: 33991022 DOI: 10.1002/chem.202100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 11/05/2022]
Abstract
In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a "DNA Aptaomics" approach to systematically design functional aptamers as well as to obtain high affinity aptamers.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Toshiki Sakamoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Naoki Tanaka
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Ryo Watanabe
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Takuya Kamimura
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kazuki Ota
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kathryn R Riley
- Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yuiko Tasaki-Handa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Masami Shibukawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
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7
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Guo X, Chen GH. Capillary electrophoresis-based methodology for screening of oligonucleotide aptamers. Biomed Chromatogr 2021; 35:e5109. [PMID: 33660332 DOI: 10.1002/bmc.5109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/28/2023]
Abstract
As a new molecular recognition element, oligonucleotide aptamer not only has higher affinity and specificity to target molecules, but also has the advantages of wide recognition range, in vitro synthesis and chemical stability compared with conventional antibodies. Since a kind of screening method termed systematic evolution of ligands by exponential enrichment (SELEX) was reported, scientists have extensively researched the methodology of how to highly and efficiently screen out aptamers from a library consisting of a large number of random oligonucleotides. Certainly capillary electrophoresis-based screening methodologies, including nonequilibrium capillary electrophoresis of equilibrium mixtures, equilibrium capillary electrophoresis of equilibrium mixtures, non-SELEX, ideal-filter capillary electrophoresis, capillary transient isotachophoresis, etc., are revolutionary. Compared with conventional SELEX, these capillary electrophoresis-based methodologies show incomparable advantages such as the single-round screening of aptamers and increased successful screening rate. Methodology studies on the screening process of aptamers are comprehensively reviewed.
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Affiliation(s)
- Xin Guo
- College of Food and Bioengineering, Jiangsu University, Zhenjiang, China.,Periodicals Agency of Jiangsu University, Zhenjiang, China
| | - Guan-Hua Chen
- College of Food and Bioengineering, Jiangsu University, Zhenjiang, China
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8
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YAMAMOTO S, KAWAGUCHI Y, KINOSHITA M, SUZUKI S. Microchip Electrophoresis Utilizing <i>In Situ</i> Photopolymerized Thrombin-Immobilized Preconcentrator Gels for Specific Entrapment and Analysis of Thrombin Aptamers. CHROMATOGRAPHY 2021. [DOI: 10.15583/jpchrom.2020.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Saito S. SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques. ANAL SCI 2021; 37:17-26. [PMID: 33132238 DOI: 10.2116/analsci.20sar18] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo Sakura, Saitama, 338-8570, Japan.
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10
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Kim AR, Choi Y, Kim SH, Moon HS, Ko JH, Yoon MY. Development of a Novel ssDNA Sequence for a Glycated Human Serum Albumin and Construction of a Simple Aptasensor System Based on Reduced Graphene Oxide (rGO). BIOSENSORS 2020; 10:E141. [PMID: 33066521 PMCID: PMC7602221 DOI: 10.3390/bios10100141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
Diabetes is one of the top 10 global causes of death. About one in 11 global adults have diabetes. As the disease progresses, the mortality rate increases, and complications can develop. Thus, early detection and effective management of diabetes are especially important. Herein, we present a novel glycated human serum albumin (GHSA) aptamer, i.e., GABAS-01, which has high affinity and specificity. The aptamer was selected by reduced graphene oxide-based systematic evolution of ligands by exponential enrichement (rGO-based SELEX) against GHSA. After five rounds of selection through gradually harsher conditions, GABAS-01 with high affinity and specificity for the target was obtained. GABAS-01 was labeled by FAM at the 5'-end and characterized by measuring the recovery of a fluorescence signal that is the result of fluorescence quenching effect of rGO. As a result, GABAS-01 had low-nanomolar Kd values of 1.748 ± 0.227 nM and showed a low limit of detection of 16.40 μg/mL against GHSA. This result shows the potential application of GABAS-01 as an effective on-site detection probe of GHSA. In addition, these properties of GABAS-01 are expected to contribute to detection of GHSA in diagnostic fields.
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Affiliation(s)
- A-Ru Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Korea; (A.-R.K.); (Y.C.); (S.-H.K.)
| | - Yeongmi Choi
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Korea; (A.-R.K.); (Y.C.); (S.-H.K.)
| | - Sang-Heon Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Korea; (A.-R.K.); (Y.C.); (S.-H.K.)
| | - Hyun-Seok Moon
- Sungsan Eng Co.ltd., Gumi 39377, Korea; (H.-S.M.); (J.-H.K.)
| | - Jae-Ho Ko
- Sungsan Eng Co.ltd., Gumi 39377, Korea; (H.-S.M.); (J.-H.K.)
| | - Moon-Young Yoon
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Korea; (A.-R.K.); (Y.C.); (S.-H.K.)
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11
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Mela I, Vallejo‐Ramirez PP, Makarchuk S, Christie G, Bailey D, Henderson RM, Sugiyama H, Endo M, Kaminski CF. DNA Nanostructures for Targeted Antimicrobial Delivery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ioanna Mela
- Department of Chemical Engineering and Biotechnology University of Cambridge Philippa Fawcett Drive Cambridge CB3 0AS UK
| | - Pedro P. Vallejo‐Ramirez
- Department of Chemical Engineering and Biotechnology University of Cambridge Philippa Fawcett Drive Cambridge CB3 0AS UK
| | - Stanislaw Makarchuk
- Department of Chemical Engineering and Biotechnology University of Cambridge Philippa Fawcett Drive Cambridge CB3 0AS UK
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology University of Cambridge Philippa Fawcett Drive Cambridge CB3 0AS UK
| | - David Bailey
- Department of Chemical Engineering and Biotechnology University of Cambridge Philippa Fawcett Drive Cambridge CB3 0AS UK
| | - Robert M. Henderson
- Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD UK
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell Material Sciences Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Masayuki Endo
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell Material Sciences Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology University of Cambridge Philippa Fawcett Drive Cambridge CB3 0AS UK
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Mela I, Vallejo‐Ramirez PP, Makarchuk S, Christie G, Bailey D, Henderson RM, Sugiyama H, Endo M, Kaminski CF. DNA Nanostructures for Targeted Antimicrobial Delivery. Angew Chem Int Ed Engl 2020; 59:12698-12702. [PMID: 32297692 PMCID: PMC7496991 DOI: 10.1002/anie.202002740] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/07/2020] [Indexed: 01/14/2023]
Abstract
We report the use of DNA origami nanostructures, functionalized with aptamers, as a vehicle for delivering the antibacterial enzyme lysozyme in a specific and efficient manner. We test the system against Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) targets. We use direct stochastic optical reconstruction microscopy (dSTORM) and atomic force microscopy (AFM) to characterize the DNA origami nanostructures and structured illumination microscopy (SIM) to assess the binding of the origami to the bacteria. We show that treatment with lysozyme-functionalized origami slows bacterial growth more effectively than treatment with free lysozyme. Our study introduces DNA origami as a tool in the fight against antibiotic resistance, and our results demonstrate the specificity and efficiency of the nanostructure as a drug delivery vehicle.
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Affiliation(s)
- Ioanna Mela
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhilippa Fawcett DriveCambridgeCB3 0ASUK
| | - Pedro P. Vallejo‐Ramirez
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhilippa Fawcett DriveCambridgeCB3 0ASUK
| | - Stanislaw Makarchuk
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhilippa Fawcett DriveCambridgeCB3 0ASUK
| | - Graham Christie
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhilippa Fawcett DriveCambridgeCB3 0ASUK
| | - David Bailey
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhilippa Fawcett DriveCambridgeCB3 0ASUK
| | - Robert M. Henderson
- Department of PharmacologyUniversity of CambridgeTennis Court RoadCambridgeCB2 1PDUK
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto UniversityKitashirakawa-oiwakecho, Sakyo-kuKyoto606-8502Japan
- Institute for Integrated Cell Material SciencesKyoto UniversityYoshida-ushinomiyacho, Sakyo-kuKyoto606-8501Japan
| | - Masayuki Endo
- Department of ChemistryGraduate School of ScienceKyoto UniversityKitashirakawa-oiwakecho, Sakyo-kuKyoto606-8502Japan
- Institute for Integrated Cell Material SciencesKyoto UniversityYoshida-ushinomiyacho, Sakyo-kuKyoto606-8501Japan
| | - Clemens F. Kaminski
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgePhilippa Fawcett DriveCambridgeCB3 0ASUK
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13
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ZHU C, ZHAO XY, YANG G, QU F. Capillary Electrophoresis Involving in High Efficiency Screening for Aptamers. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [PMCID: PMC7219368 DOI: 10.1016/s1872-2040(20)60014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a universal technology for aptamer' screening. Accurate and efficient screening methods and strategy design are the key to success. This review briefly summarizes capillary electrophoresis (CE) involving in the efficient screening for aptamers in our group since 2007, including the application of CE in pre-screening, screening and post-screening process, classification and screening strategies against different protein targets, multiple screening modes, and screening for multi-scale targets. Finally, combined with the current progresses of aptamer screening, some remaining issues are discussed and the development prospects are proposed.
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14
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Haraga T, Tsujimura H, Miyauchi S, Kamimura T, Shibukawa M, Saito S. Purification of anionic fluorescent probes through precise fraction collection with a two-point detection system using multiple-stacking preparative capillary transient isotachophoresis. Electrophoresis 2020; 41:1152-1159. [PMID: 32253765 DOI: 10.1002/elps.201900399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 11/11/2022]
Abstract
A novel combination of CE-based separation techniques was used for the precise fractionation of ionic compounds from impurities. The combination of on-capillary concentration and separation using transient isotachophoresis, with multiple injections and a two-point detection system provided higher efficiency, and accuracy at a microliter-scale injection volume, than when CE was individually used for purification. In this paper, we present successful applications of the CE fractionation techniques for the purification of fluorescein, fluorescein-4-isothiocyanate, two fluorescent metal ion probes, and a fluorescein-modified DNA aptamer. The purity of the isolated fluorescent probes ranged from 95 to 99%. Such high purity could not be achieved using chromatographic purification techniques. With relatively low dilution factors of 6-9, the purified probe solutions were practical for use as purified stock solutions. In addition, the fluorescein-modified DNA aptamer purified by our method was successfully used in a thrombin binding assay. The method developed was useful for the purification of anionic fluorescent reagents to be of ultratrace analytical grade for use with CE-LIF.
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Affiliation(s)
- Tomoko Haraga
- Department of Decommissioning and Waste Management, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki, 319-1195, Japan
| | - Hiroto Tsujimura
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Saori Miyauchi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Takuya Kamimura
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Masami Shibukawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
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15
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Binding and Structural Properties of DNA Aptamers with VEGF-A-Mimic Activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1145-1152. [PMID: 32059340 PMCID: PMC7016029 DOI: 10.1016/j.omtn.2019.12.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022]
Abstract
Vascular endothelial growth factors (VEGFs) are hypoxia-inducible secreted proteins to promote angiogenesis, in which VEGF-A is an important molecule that binds and activates VEGF receptor-1 (VEGFR-1) and VEGFR-2. In this study, two DNA aptamers, Apt01 and Apt02, were successfully isolated by alternating consecutive systematic evolution of ligands by exponential enrichment (SELEX) against VEGFR-1 and -2 using deep sequencing analysis in an early selection round. Their binding affinities for VEGFR-2 were lower than that of VEGFR-1, which is similar to that of VEGF-A. Structural analyses with the measurements of circular dichroism spectra and ultraviolet melting curve showed that Apt01 possessed the stem-loop structure in the molecule, whereas Apt02 formed G-quadruplex structures. In addition, Apt02 accelerated a tube formation of human umbilical vein endothelial cells faster than Apt01, which was affected by difference of binding affinity and nuclease resistance due to G-quadruplex structures. These results demonstrated that Apt02 might have a potential to function as an alternative to VEGF-A.
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16
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Affiliation(s)
- Keitaro YOSHIMOTO
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
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17
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Wakui K, Abe A, Yoshitomi T, Furusho H, Yoshimoto K. High Enrichment of Nucleobase-modified Aptamers in Early Selection Rounds by Microbeads-assisted Capillary Electrophoresis SELEX. ANAL SCI 2019; 35:585-588. [PMID: 31080213 DOI: 10.2116/analsci.18sdn04] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nucleobase-modified aptamers are attractive candidates for diagnostic and therapeutic agents due to the high affinity, stability and functionality. However, since even conventional SELEX requires many selection rounds, acquisition of modified aptamers is much more laborious. Herein, microbeads-assisted capillary electrophoresis (MACE)-SELEX was applied against thrombin using the indole-modified DNA library. After only three selection rounds, we successfully enriched the modified aptamers and they showed slower off-rate than reported aptamers, suggesting MACE-SELEX is a promising approach for rapid identification of modified aptamers.
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Affiliation(s)
- Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Akihito Abe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Hitoshi Furusho
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo.,Chemical General Division, Nissan Chemical Industries, Ltd
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo.,JST, PRESTO, The University of Tokyo
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18
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Zhu C, Yang G, Ghulam M, Li L, Qu F. Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers. Biotechnol Adv 2019; 37:107432. [PMID: 31437572 DOI: 10.1016/j.biotechadv.2019.107432] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/24/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023]
Abstract
Aptamers have drawn considerable attention as newly emerging molecular recognition elements in clinical diagnostics, drug delivery, therapeutics, environmental monitoring, and food safety analyses. As the in vitro screening antibody analogs, aptamers are enabled to recognize various types of targets with high affinity and specificity like or even superior to antibodies. However, the restrictions and inefficiency of selection have been hampering their wider application. Among various modified systematic evolution of ligands by exponential enrichment (SELEX) methods, capillary electrophoresis (CE)-SELEX holds multiple functions and advantages with the powerful qualitative and quantitative analysis capabilities, less consumption of sample and analytical reagent, natural binding environment, higher screening efficiency, and availability in multiple modes. This review summarizes the key developments in the area of CE-SELEX by leading research groups, including our teams' ten years of research and experience to help researchers fully understand and utilize CE-SELEX. Aptamers' history, applications, as well as the SELEX developments, have been briefly described; the advantages of CE-SELEX are highlighted compared with the conventional SELEX methods. Further, we describe some essential CE-SELEX models and provide an overview of the CE-SELEX, including the targets and ssDNA library, every technical point in the selection process, and post-SELEX protocol. We expect this review will inspire more researchers to have insight into the screening problems from CE-SELEX viewpoint and will help to improve the selection efficiency and probability of success to meet the growing needs of aptamers' discovery in bioanalytical and medical fields.
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Affiliation(s)
- Chao Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Murtaza Ghulam
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China.
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19
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High-efficiency selection of aptamers for bovine lactoferrin by capillary electrophoresis and its aptasensor application in milk powder. Talanta 2019; 205:120088. [PMID: 31450439 DOI: 10.1016/j.talanta.2019.06.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/14/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
Abstract
Capillary electrophoresis-based systematic evolution of ligands by exponential enrichment (CE-SELEX) is a high-efficient technique for aptamers selection, and has been evolved into many modes. In this study, we obtained the aptamer against bovine lactoferrin (BLF) with high affinity (dissociation constant, Kd = 20.74 ± 6.89 nM) and good specificity (>1000 folds) using single step CE-SELEX (ssCE-SELEX) mode. In the selection process, ssCE demonstrated high-efficiency selection with bulk Kd reaching at 0.19 ± 0.04 μM by only two rounds, as compared to capillary zone electrophoresis (CZE) mode with Kd of 0.39 ± 0.03 μM. Next-generation sequencing (NGS) was performed by two methods of high output (Hiseq) and medium output (Miseq) with different sequencing depths, and their same results of high-frequency sequences confirmed the reliability of the obtained sequences. Through affinity analysis, the primer region and single base mutation (SBM) were observed to affect the sequence structure and to result in affinity change. Besides, molecular dynamics (MD) simulation was performed to validate the binding affinity of the candidates with BLF by analyzing binding sites, interaction forces, and binding free energy. Moreover, BLF detection in milk powder matrices was completed successfully with the optimized CE-aptasensor. The signal response was in a good linear relationship (R2 = 0.9930) with 4-128 nM of BLF and the detection limit was 1 nM. The obtained results of BLF in four milk powder samples were in an acceptable agreement with the labeled concentrations. This study presented a completed CE based process including aptamers selection, affinity characterization, and detection application, which also validated the high-efficiency selection of ssCE-SELEX mode.
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20
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Yoshitomi T, Wayama F, Kimura K, Wakui K, Furusho H, Yoshimoto K. Screening of DNA Signaling Aptamer from Multiple Candidates Obtained from SELEX with Next-generation Sequencing. ANAL SCI 2019; 35:113-116. [PMID: 30626772 DOI: 10.2116/analsci.18sdn05] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here, we demonstrated a strategy for developing signaling aptamers, based on screening of signaling aptamers from multiple aptamer candidates obtained by SELEX with next generation sequencing. Among aptamer candidates labelled by 6-carboxyfluorescein and quencher at both end termini, there is the possibility of discovering a potent signaling aptamer. In this study, we discovered DNA signaling aptamers against VEGFR-1. This strategy has the potential for signaling aptamer discovery without the extremely laborious task of optimization of oligodeoxynucleotide modifications.
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Affiliation(s)
- Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Fumiya Wayama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Keiko Kimura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | | | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo.,JST, PRESTO, The University of Tokyo
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21
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Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection. Anal Chim Acta 2019; 1070:112-122. [PMID: 31103164 DOI: 10.1016/j.aca.2019.04.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 12/29/2022]
Abstract
Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has proven to be an effective technique for aptamers selection. In this study, we present an online reaction based convenient single-step CE-SELEX (ssCE-SELEX) mode with human thrombin (H-Thr) as a model target. The selection progress was monitored through bulk Kd analysis, which showed more than a 1000-fold improvement over the initial library after two rounds of selection. Three selected candidate sequences presented high binding affinities against H-Thr with nanomolar (nM) Kd determined by nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM, 56.4-177.1 nM) and CE based non-linear fitting (CE-NLF, 98.2-199.7 nM). They also exhibited high specificities towards H-Thr compared with bovine thrombin, IgG, lysozyme, and lactoferrin. Meanwhile, the Kd results by isothermal titration calorimetry (ITC) confirmed the effective CE in measuring the aptamer affinity. In addition, three candidates were applied as aptasensors in the AuNPs based colorimetric assay, which showed visible color change and good linear relationships (R2 > 0.93) with H-Thr concentration. Furthermore, molecular dynamics (MD) simulation was performed to validate the binding of the three candidates with H-Thr by binding sites and binding free energy. The ssCE-SELEX method avoids off-line incubation, saves time and sample, and may provide a universal and convenient method for aptamers selection.
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22
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Riley KR, El Hadri H, Tan J, Hackley VA, MacCrehan WA. High separation efficiency of gold nanomaterials of different aspect ratio and size using capillary transient isotachophoresis. J Chromatogr A 2019; 1598:216-222. [PMID: 30948041 DOI: 10.1016/j.chroma.2019.03.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/17/2019] [Accepted: 03/23/2019] [Indexed: 11/25/2022]
Abstract
Two modes of capillary electrophoresis (CE), capillary zone electrophoresis (CZE) and capillary transient isotachophoresis (ctITP), were compared for the detection and separation of spherical gold nanoparticles (AuNPs) and gold nanorods (AuNRs). The development of ctITP using two different leading ions is described. Overall, when compared to traditional capillary zone electrophoresis (CZE), ctITP resulted in improved peak shape and peak efficiency. Specifically, the number of theoretical plates for AuNR samples increased by a factor of 2-2.5 depending on the choice of leading ion. Further, using ctITP two AuNRs differing by aspect ratio were baseline resolved, whereas the same AuNRs could not be separated using CZE or other techniques like single particle inductively coupled plasma mass spectrometry (spICP-MS) and asymmetric flow field-flow fractionation (AF4). The results of this study demonstrate that ctITP is an efficient on-line technique for the improved detection and separation of gold nanomaterials in CE.
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Affiliation(s)
- Kathryn R Riley
- National Institute of Standards and Technology, Material Measurement Laboratory - Chemical Sciences Division, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
| | - Hind El Hadri
- National Institute of Standards and Technology, Material Measurement Laboratory - Materials Measurement Science Division, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jiaojie Tan
- National Institute of Standards and Technology, Material Measurement Laboratory - Materials Measurement Science Division, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Vincent A Hackley
- National Institute of Standards and Technology, Material Measurement Laboratory - Materials Measurement Science Division, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - William A MacCrehan
- National Institute of Standards and Technology, Material Measurement Laboratory - Chemical Sciences Division, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
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23
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Wakui K, Yoshitomi T, Yamaguchi A, Tsuchida M, Saito S, Shibukawa M, Furusho H, Yoshimoto K. Rapidly Neutralizable and Highly Anticoagulant Thrombin-Binding DNA Aptamer Discovered by MACE SELEX. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:348-359. [PMID: 30986696 PMCID: PMC6462803 DOI: 10.1016/j.omtn.2019.03.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 02/07/2023]
Abstract
We present a rapidly neutralizable and highly anticoagulant thrombin-binding aptamer with a short toehold sequence, originally discovered by systematic evolution of ligands by exponential enrichment (SELEX) with microbead-assisted capillary electrophoresis (MACE). MACE is a novel CE-partitioning method for SELEX and able to separate aptamers from a library of unbound nucleic acids, where the aptamer and target complexes can be detected reliably and partitioned with high purity even in the first selection cycle. Three selection rounds of MACE-SELEX discovered several TBAs with a nanomolar affinity (Kd = 4.5-8.2 nM) that surpasses previously reported TBAs such as HD1, HD22, and NU172 (Kd = 118, 13, and 12 nM, respectively). One of the obtained aptamers, M08, showed a 10- to 20-fold longer prolonged clotting time than other anticoagulant TBAs, such as HD1, NU172, RE31, and RA36. Analyses of the aptamer and thrombin complexes using both bare and coated capillaries suggested that a large number of efficient aptamers are missed in conventional CE-SELEX because of increased interaction between the complex and the capillary. In addition, the toehold-mediated rapid antidote was designed for safe administration. The efficient aptamer and antidote system developed in the present study could serve as a new candidate for anticoagulant therapy.
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Affiliation(s)
- Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Akane Yamaguchi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Maho Tsuchida
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masami Shibukawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Hitoshi Furusho
- Chemical General Division, Nissan Chemical Industries, Ltd., 2-10-2 Tsuboi-nishi, Funabashi, Chiba 274-8507, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; JST, PRESTO, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.
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24
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Hirose K, Tsuchida M, Asakura H, Wakui K, Yoshimoto K, Iida K, Sato M, Shibukawa M, Suganuma M, Saito S. A single-round selection of selective DNA aptamers for mammalian cells by polymer-enhanced capillary transient isotachophoresis. Analyst 2018; 142:4030-4038. [PMID: 28875191 DOI: 10.1039/c7an00909g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A single-round DNA aptamer selection for mammalian cells was successfully achieved for the first time using a capillary electrophoresis (CE)-based methodology called polymer-enhanced capillary transient isotachophoresis (PectI). The PectI separation yielded a single peak for the human lung cancer cell line (PC-9) complexed with DNA aptamer candidates, which was effectively separated from a free randomized DNA library peak, ensuring no contamination from free DNA in the PC-9-DNA aptamer complex fraction. The DNA aptamer candidates obtained after a single-round selection employing counter selection with HL-60 were proven to bind selectively and form kinetically stable complexes with PC-9 cells. Interestingly, most aptamer candidates showed high binding ability (Kd = 70-350 nM) with different extents of binding on the cell surface. These facts proved that a single-round selection for mammalian cells by PectI is feasible to obtain various types of aptamer candidates, which have high-affinity even for non-overexpressed but unique targets on the cell surface in addition to overexpressed targets.
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Affiliation(s)
- Kazuki Hirose
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.
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25
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Zhu C, Wang X, Li L, Hao C, Hu Y, Rizvi AS, Qu F. Online reaction based single-step CE for Protein-ssDNA complex obtainment to assist aptamer selection. Biochem Biophys Res Commun 2018; 506:169-175. [PMID: 30340834 DOI: 10.1016/j.bbrc.2018.08.189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/07/2023]
Abstract
CE application in aptamer selection (CE-SELEX) shows more advantages than other selection methods. In this study, an online reaction based single-step CE (ssCE) mode was employed for fast obtaining protein-ssDNA complex. Using human thrombin (H-Thr) and its aptamer Apt29 as models, we accomplished the procedures of mixing, reaction, separation, detection and complex collection in single step online process, which took about 10 min to obtain the H-Thr/Apt29 complex. Important factors, affecting the aptamer and H-Thr interaction (buffer, ratio of aptamer and H-Thr amount), and complex separation and collection (voltage and temperature) were discussed. Later, the online reaction of H-Thr with an 80 nt ssDNA library was realized under optimized conditions, and the H-Thr/ssDNA complex was collected and subjected to PCR. By analyzing the PCR product through capillary gel electrophoresis, the resulting approximative 80 nt DNA length validated the ssDNA sequence in complex. To confirm the availability of ssCE mode, two ssDNA libraries with different lengths (56 nt and 82 nt ssDNA) and three proteins (platelet derived growth factor, PDGF-BB; lactoferrin protein, LF; and single-strand DNA binding protein, SSB) were utilized. Their complex peaks were also observed in electropherograms as expected. Additionally, the online incubation of ssDNA and H-Thr was achieved by stopping the separation voltage for some time when ssDNA passed the H-Thr zone. Our results show the ssCE mode has apparent merits of saving time and sample cost for aptamer selection against protein targets.
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Affiliation(s)
- Chao Zhu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Xiaoqian Wang
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Linsen Li
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Chenxu Hao
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Youhao Hu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Aysha Sarfraz Rizvi
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Feng Qu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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26
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Preparative concentration of nucleic acids fragments by capillary isotachophoretic analyzer. J Chromatogr A 2018; 1548:100-103. [DOI: 10.1016/j.chroma.2018.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 01/07/2023]
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27
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Datinská V, Voráčová I, Schlecht U, Berka J, Foret F. Recent progress in nucleic acids isotachophoresis. J Sep Sci 2017; 41:236-247. [DOI: 10.1002/jssc.201700878] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Vladimíra Datinská
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
- Masaryk University; Faculty of Science; Brno Czech Republic
| | - Ivona Voráčová
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
| | | | - Jan Berka
- Roche Sequencing Solutions, Inc; Pleasanton CA USA
| | - František Foret
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
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28
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Enomoto J, Kageyama T, Osaki T, Bonalumi F, Marchese F, Gautieri A, Bianchi E, Dubini G, Arrigoni C, Moretti M, Fukuda J. Catch-and-Release of Target Cells Using Aptamer-Conjugated Electroactive Zwitterionic Oligopeptide SAM. Sci Rep 2017; 7:43375. [PMID: 28266533 PMCID: PMC5339905 DOI: 10.1038/srep43375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/23/2017] [Indexed: 11/18/2022] Open
Abstract
Nucleic acid aptamers possess attractive features such as specific molecular recognition, high-affinity binding, and rapid acquisition and replication, which could be feasible components for separating specific cells from other cell types. This study demonstrates that aptamers conjugated to an oligopeptide self-assembled monolayer (SAM) can be used to selectively trap human hepatic cancer cells from cell mixtures containing normal human hepatocytes or human fibroblasts. Molecular dynamics calculations have been performed to understand how the configurations of the aptamers are related to the experimental results of selective cell capture. We further demonstrate that the captured hepatic cancer cells can be detached and collected along with electrochemical desorption of the oligopeptide SAM, and by repeating these catch-and-release processes, target cells can be enriched. This combination of capture with aptamers and detachment with electrochemical reactions is a promising tool in various research fields ranging from basic cancer research to tissue engineering applications.
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Affiliation(s)
- Junko Enomoto
- Graduate School of Engineering, Yokohama National University, Japan
| | - Tatsuto Kageyama
- Graduate School of Engineering, Yokohama National University, Japan
| | - Tatsuya Osaki
- Graduate School of Engineering, Yokohama National University, Japan
| | - Flavia Bonalumi
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
| | - Francesca Marchese
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
| | - Alfonso Gautieri
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy
| | - Elena Bianchi
- Department of Chemistry, Politecnico di Milan, Italy
| | | | - Chiara Arrigoni
- Cell and Tissue Engineering Laboratory, IRCCS Galeazzi Orthopaedic Institute, Italy
| | - Matteo Moretti
- Cell and Tissue Engineering Laboratory, IRCCS Galeazzi Orthopaedic Institute, Italy
- Regenerative Medicine Technologies Lab, Ente Ospedaliero Cantonale, Switzerland
- Swiss Institute for Regenerative Medicine, Switzerland
- Cardiocentro Ticino, Switzerland
| | - Junji Fukuda
- Graduate School of Engineering, Yokohama National University, Japan
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