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Matsuo M, Wakui K, Inami Y, Furukawa A, Sato S, Yoshimoto K. Proficiently partitioning of bioactive peptide-ssDNA conjugates by microbead-assisted capillary electrophoresis (MACE). Anal Biochem 2024; 687:115452. [PMID: 38158105 DOI: 10.1016/j.ab.2023.115452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/01/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Low-molecular drug discovery using DNA-encoded chemical library (DEL) is a powerful technology, although improving the partitioning efficiency of affinity ligands from DEL remains a challenge. Here, we assessed the usefulness of microbead-assisted capillary electrophoresis (MACE) for partitioning peptide-oligonucleotide conjugates (POCs), in which high selection pressure is applied because of different mobility of target-modified beads and POCs during CE. Despite their different charge characteristics, all POCs were well separated from the beads. When bead extraction was performed, the tagged DNA amplification was observed only in the couple of a ligand/target, suggesting proficiently specific partitioning of peptide ligands was accomplished using MACE.
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Affiliation(s)
- Muneyuki Matsuo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan; Graduate School of Integrated Science for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - 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
| | - Yuuki Inami
- LinkBIO Co., Ltd., 5270, Terada, Toride, Ibaraki, 302-0021, Japan
| | - Akihiro Furukawa
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa, Tokyo, 140-8710, Japan
| | - Seiji Sato
- R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa, Tokyo, 140-8710, 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; LinkBIO Co., Ltd., 5270, Terada, Toride, Ibaraki, 302-0021, Japan.
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2
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Deng L, Fu Q, Zhang Y, Shui F, Tang J, Wu J, Zeng J. Study of molecular interactions by nonequilibrium capillary electrophoresis of equilibrium mixtures: Originations, developments, and applications. Electrophoresis 2023; 44:1664-1673. [PMID: 37621032 DOI: 10.1002/elps.202300166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023]
Abstract
Molecular interactions play a vital role in regulating various physiological and biochemical processes in vivo. Kinetic capillary electrophoresis (KCE) is an analytical platform that offers significant advantages in studying the thermodynamic and kinetic parameters of molecular interactions. It enables the simultaneous analysis of these parameters within an interaction pattern and facilitates the screening of binding ligands with predetermined kinetic parameters. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was the first proposed KCE method, and it has found widespread use in studying molecular interactions involving proteins/aptamers, proteins/small molecules, and peptides/small molecules. The successful applications of NECEEM have demonstrated its promising potential for further development and broader application. However, there has been a dearth of recent reviews on NECEEM. To address this gap, our study provides a comprehensive description of NECEEM, encompassing its origins, development, and applications from 2015 to 2022. The primary focus of the applications section is on aptamer selection and screening of small-molecule ligands. Furthermore, we discuss important considerations in NECEEM experimental design, such as buffer suitability, detector selection, and protein adsorption. By offering this thorough review, we aim to contribute to the understanding, advancement, and wider utilization of NECEEM as a valuable tool for studying molecular interactions and facilitating the identification of potential ligands and targets.
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Affiliation(s)
- Li Deng
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Qifeng Fu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Yujie Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Fan Shui
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jia Tang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jianming Wu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
- School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jing Zeng
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
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3
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Walter J, Eludin Z, Drabovich AP. Redefining serological diagnostics with immunoaffinity proteomics. Clin Proteomics 2023; 20:42. [PMID: 37821808 PMCID: PMC10568870 DOI: 10.1186/s12014-023-09431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lack of universal reference standards, potential cross-reactivity, and challenges with multiplexing the complete panel of human immunoglobulin isotypes and subclasses. Redesign of conventional serological tests to include multiplex quantification of immunoglobulin isotypes and subclasses, utilize universal reference standards, and minimize cross-reactivity and non-specific binding will facilitate the development of assays with higher diagnostic specificity. Improved serological assays with higher diagnostic specificity will enable screenings of asymptomatic populations and may provide earlier detection of infectious diseases, autoimmune disorders, and cancer. In this review, we present the major clinical needs for serological diagnostics, overview conventional immunoassay detection techniques, present the emerging immunoassay detection technologies, and discuss in detail the advantages and limitations of mass spectrometry and immunoaffinity proteomics for serological diagnostics. Finally, we explore the design of novel immunoaffinity-proteomic assays to evaluate cell-mediated immunity and advance the sequencing of clinically relevant immunoglobulins.
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Affiliation(s)
- Jonathan Walter
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zicki Eludin
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
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4
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Ye W, Zhang Z, Wang C, Feng Z, Hu Z, Liu Q, Wu T. Detection of small molecules by extending the terminal protection to the polymerase. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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5
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Xiao Q, Chen M, Nie W, Xie F, Yu X, Ma C. A Fluorescent Biosensor for Streptavidin Detection Based on Double-Hairpin DNA-Templated Copper Nanoparticles. BIOSENSORS 2023; 13:168. [PMID: 36831934 PMCID: PMC9953726 DOI: 10.3390/bios13020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
In this paper, we developed a sensitive, label-free and facile fluorescent strategy for detecting streptavidin (SA) based on double-hairpin DNA-templated copper nanoparticles (CuNPs) and terminal protection of small molecule-linked DNA. Herein, a special DNA hairpin probe was designed and synthesized, which contained two poly T single-stranded loops and a nick point in the middle of the stem. Inspired by the concept of the terminal protection interaction, the specific binding of SA to the biotinylated DNA probe can prevent the exonuclease degradation and keep the integrity of DNA probe, which can be used for synthesizing fluorescent CuNPs as a template. Conversely, the DNA probe would be digested by exonucleases and therefore, would fail to form CuNPs without SA. After systematic optimization, the detection range of SA concentration is from 0.5 to 150 nM with a low detection limit of 0.09 nM. Additionally, the proposed method was also successfully applied in the biological samples. Finally, the proposed method is sensitive, effective and simple, and can be potentially applied for predicting diseases and discovering new drugs.
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Affiliation(s)
- Qiangsheng Xiao
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Mingjian Chen
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Wanpin Nie
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Fengjiao Xie
- The Third Affiliated Hospital of Southern Medical University, Guangzhou 510640, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410017, China
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6
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Cai B, Mhetre AB, Krusemark CJ. Selection methods for proximity-dependent enrichment of ligands from DNA-encoded libraries using enzymatic fusion proteins. Chem Sci 2023; 14:245-250. [PMID: 36687357 PMCID: PMC9811540 DOI: 10.1039/d2sc05495g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we report a selection approach to enrich ligands from DNA-encoded libraries (DELs) based on proximity to an enzymatic tag on the target protein. This method involves uncaging or installation of a biotin purification tag on the DNA construct either through photodeprotection of a protected biotin group using a light emitting protein tag (nanoluciferase) or by acylation using an engineered biotin ligase (UltraID). This selection does not require purification of the target protein and results in improved recovery and enrichment of DNA-linked ligands. This approach should serve as a general and convenient tool for molecular discovery with DELs.
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Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| | - Amol B. Mhetre
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue UniversityWest LafayetteIN 47907USA
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7
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Fu Z, Rais Y, Dara D, Jackson D, Drabovich AP. Rational Design and Development of SARS-CoV-2 Serological Diagnostics by Immunoprecipitation-Targeted Proteomics. Anal Chem 2022; 94:12990-12999. [PMID: 36095284 PMCID: PMC9523617 DOI: 10.1021/acs.analchem.2c01325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Current design of serological tests utilizes conservative
immunoassay
approaches and is focused on fast and convenient assay development,
throughput, straightforward measurements, and affordability. Limitations
of common serological assays include semiquantitative measurements,
cross-reactivity, lack of reference standards, and no differentiation
between human immunoglobulin subclasses. In this study, we suggested
that a combination of immunoaffinity enrichments with targeted proteomics
would enable rational design and development of serological assays
of infectious diseases, such as COVID-19. Immunoprecipitation-targeted
proteomic assays allowed for sensitive and specific measurements of
NCAP_SARS2 protein with a limit of detection of 313 pg/mL in serum
and enabled differential quantification of anti-SARS-CoV-2 antibody
isotypes (IgG, IgA, IgM, IgD, and IgE) and individual subclasses (IgG1-4
and IgA1-2) in plasma and saliva. Simultaneous evaluation of the numerous
antigen–antibody subclass combinations revealed a receptor-binding
domain (RBD)-IgG1 as a combination with the highest diagnostic performance.
Further validation revealed that anti-RBD IgG1, IgG3, IgM, and IgA1
levels were significantly elevated in convalescent plasma, while IgG2,
IgG4, and IgA2 were not informative. Anti-RBD IgG1 levels in convalescent
(2138 ng/mL) vs negative (95 ng/mL) plasma revealed 385 ng/mL as a
cutoff to detect COVID-19 convalescent plasma. Immunoprecipitation-targeted
proteomic assays will facilitate improvement and standardization of
the existing serological tests, enable rational design of novel tests,
and offer tools for the comprehensive investigation of immunoglobulin
subclass cooperation in immune response.
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Affiliation(s)
- Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Delaram Dara
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Dana Jackson
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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8
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Chumak A, Khodzhaeva R, Kharchenko O, Kotlyar V, Kolomoitsev O, Doroshenko A. Complexation of 1,3-dihetaryl-5-phenyl-2-pyrazoline Derivatives with Polyvalent Metal Ions: Quantum Chemical Modeling and Experimental Investigation. FRENCH-UKRAINIAN JOURNAL OF CHEMISTRY 2022. [DOI: 10.17721/fujcv10i1p155-174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
1,3,5-Triaryl-2-pyrazoline derivatives with a pyridine ring in position 1 and 2-benzimidazolyl or 2-benzothiazolyl bicycles in position 3 were synthesized. Spectral properties in solvents of similar polarity, i.e. aprotic acetonitrile and in protic methanol, were studied, complexation with cadmium and mercury ions in acetonitrile was elucidated as well. Quantum-chemical modeling with application of the elements of Bader's atoms-in-molecules (AIM) theory of the title molecules conformational structure and 1:1 stoichiometry complexes formed with polyvalent metals of various nature (Mg, Zn, Cd, Pb, Hg, Ba) was conducted. The principal possibility of “nitrogen-sulfur” switching of the metal ions binding sites for the benzothiazole derivative was revealed, and makes possible to classify this compound as “smart ligand”.
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9
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Kim H, Lee S, Yoon J, Song J, Park HG. CRISPR/Cas12a collateral cleavage activity for simple and rapid detection of protein/small molecule interaction. Biosens Bioelectron 2021; 194:113587. [PMID: 34455224 DOI: 10.1016/j.bios.2021.113587] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 12/26/2022]
Abstract
To realize the full potential of the CRISPR/Cas system and expand its applicability up to the detection of molecular interactions, we herein describe a novel method to identify protein/small molecule interactions by utilizing the CRISPR/Cas12a collateral cleavage activity. This technique employs a single-stranded activator DNA modified with a specific small molecule, which would switch on the CRISPR/Cas12a collateral cleavage activity upon binding to crRNA within the CRISPR/Cas12a system. When the target protein binds to the small molecule on the activator DNA, the bound protein sterically hinders the access of the activator DNA to crRNA, thereby promoting less collateral cleavage activity of CRISPR/Cas12a. As a consequence, fewer reporter probes nearby are cleaved to produce accordingly reduced fluorescence signals in response to target protein. Based on this unique design principle, the two model protein/small molecule interactions, streptavidin/biotin and anti-digoxigenin/digoxigenin, were successfully determined down to 0.03 nM and 0.09 nM, respectively, with a fast and simple detection workflow (11 min). The practical applicability of this method was also verified by reliably detecting target streptavidin spiked in heterogeneous human serum. This work would provide great insight to construct novel strategies to identify protein/small molecule interaction by making the most of the CRISPR/Cas12a system beyond its superior capabilities in genome editing and molecular diagnostics.
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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10
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Huang Y, Li X. Recent Advances on the Selection Methods of DNA-Encoded Libraries. Chembiochem 2021; 22:2384-2397. [PMID: 33891355 DOI: 10.1002/cbic.202100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/23/2021] [Indexed: 12/15/2022]
Abstract
DNA-encoded libraries (DEL) have come of age and become a major technology platform for ligand discovery in both academia and the pharmaceutical industry. Technological maturation in the past two decades and the recent explosive developments of DEL-compatible chemistries have greatly improved the chemical diversity of DELs and fueled its applications in drug discovery. A relatively less-covered aspect of DELs is the selection method. Typically, DEL selection is considered as a binding assay and the selection is conducted with purified protein targets immobilized on a matrix, and the binders are separated from the non-binding background via physical washes. However, the recent innovations in DEL selection methods have not only expanded the target scope of DELs, but also revealed the potential of the DEL technology as a powerful tool in exploring fundamental biology. In this Review, we first cover the "classic" DEL selection methods with purified proteins on solid phase, and then we discuss the strategies to realize DEL selections in solution phase. Finally, we focus on the emerging approaches for DELs to interrogate complex biological targets.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F., Building 17W, Hong Kong Science and Technology Parks, New Territories, Hong Kong SAR, China
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Li Y, Yu F, Chen S, Zhang N, Wang H, Zhao Q. Immunoassay of Small Molecule Mediated by a Triply Functional DNA. Anal Chem 2021; 93:4794-4799. [DOI: 10.1021/acs.analchem.0c05386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaokun Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310000, China
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12
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Detection of Streptavidin Based on Terminal Protection and Cationic Conjugated Polymer-Mediated Fluorescence Resonance Energy Transfer. Polymers (Basel) 2021; 13:polym13050725. [PMID: 33673477 PMCID: PMC7956837 DOI: 10.3390/polym13050725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
In this paper, a fast and simple strategy for sensitive detection of streptavidin (SA) was proposed based on terminal protection of small molecule-linked DNA and cationic conjugated polymer-mediated fluorescence resonance energy transfer (FRET). In principle, we designed a biotin-labelled DNA probe (P1) as the recognitive probe of SA, along with a complementary DNA probe (P2) to form double-stranded DNA (dsDNA) with P1. SYBR Green I (SG I) as a fluorescent dye was further used to specifically bind to dsDNA to emit stronger fluorescence. The cationic poly[(9,9-bis(6′-N,N,N-triethy-lammonium)hexyl) fluorenylene phenylene dibromide] (PFP) acted as the donor to participate in the FRET and transfer energy to the recipient SG I. In the absence of SA, P1 could not hybridize with P2 to form dsDNA and was digested by exonuclease I (Exo I); thus, only a weak FRET signal would be observed. In the presence of SA, biotin could specifically bind to SA, which protected P1 from Exo I cleavage. Then, P1 and P2 were hybridized into dsDNA. Therefore, the addition of SG I and PFP led to obvious FRET signal due to strong electrostatic interactions. Then, SA can be quantitatively detected by monitoring FRET changes. As the whole reagent reaction was carried out in 1.5 mL EP and detected in the colorimetric dish, the operation process of the detection system was relatively simple. The response time for each step was also relatively short. In this detection system, the linear equation was obtained for SA from 0.1 to 20 nM with a low detection limit of 0.068 nM (S/N = 3). In addition, this strategy has also achieved satisfactory results in the application of biological samples, which reveals the application prospect of this method in the future.
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13
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Conole D, H Hunter J, J Waring M. The maturation of DNA encoded libraries: opportunities for new users. Future Med Chem 2021; 13:173-191. [PMID: 33275046 DOI: 10.4155/fmc-2020-0285] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA-encoded combinatorial libraries (DECLs) represent an exciting new technology for high-throughput screening, significantly increasing its capacity and cost-effectiveness. Historically, DECLs have been the domain of specialized academic groups and industry; however, there has recently been a shift toward more drug discovery academic centers and institutes adopting this technology. Key to this development has been the simplification, characterization and standardization of various DECL subprotocols, such as library design, affinity screening and data analysis of hits. This review examines the feasibility of implementing DECL screening technology as a first-time user, particularly in academia, exploring the some important considerations for this, and outlines some applications of the technology that academia could contribute to the field.
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Affiliation(s)
- Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London, W12 0BZ, UK
| | - James H Hunter
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural & Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural & Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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14
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Lee CY, Kim HY, Kim S, Park KS, Park HG. A simple and sensitive detection of small molecule-protein interactions based on terminal protection-mediated exponential strand displacement amplification. Analyst 2019; 143:2023-2028. [PMID: 29634063 DOI: 10.1039/c8an00099a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein describe a simple and sensitive strategy to detect a small molecule-protein interaction based on terminal protection-mediated exponential strand displacement amplification (eSDA). In principle, the small molecule linked to a DNA probe protects the DNA probe against the exonuclease I-catalyzed degradation after its binding to the corresponding target protein. The protected DNA probe then serves as a template to promote eSDA. Consequently, a large number of duplexes are produced, which leads to a high fluorescence from a double-stranded DNA specific fluorescent dye, SYBR Green I. As a model system to prove this sensing strategy, the interaction between biotin and streptavidin (SA), which is known to be the strongest among the non-covalent biological interactions, was selected and its analytical performance was thoroughly investigated. As a result, SA was sensitively detected with the limit of detection of 16 pM. In addition, the practical applicability of this method was successfully demonstrated by reliably determining the SA in human serum.
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Affiliation(s)
- Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21 + program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
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15
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Alhajj N, Chee CF, Wong TW, Rahman NA, Abu Kasim NH, Colombo P. Lung cancer: active therapeutic targeting and inhalational nanoproduct design. Expert Opin Drug Deliv 2018; 15:1223-1247. [DOI: 10.1080/17425247.2018.1547280] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nasser Alhajj
- Non-Destructive Biomedical and Pharmaceutical Research Centre, iPROMISE, Universiti Teknologi MARA Selangor, Puncak Alam, Malaysia
| | - Chin Fei Chee
- Nanotechnology & Catalysis Research Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Tin Wui Wong
- Non-Destructive Biomedical and Pharmaceutical Research Centre, iPROMISE, Universiti Teknologi MARA Selangor, Puncak Alam, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Noor Hayaty Abu Kasim
- Wellness Research Cluster, Institute of Research Management & Monitoring, University of Malaya, Kuala Lumpur, Malaysia
| | - Paolo Colombo
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
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16
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Kochmann S, Le ATH, Hili R, Krylov SN. Predicting efficiency of NECEEM‐based partitioning of protein binders from nonbinders in DNA‐encoded libraries. Electrophoresis 2018; 39:2991-2996. [DOI: 10.1002/elps.201800270] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sven Kochmann
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
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17
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Kim H, Lee CY, Song J, Yoon J, Park KS, Park HG. Protein-induced fluorescence enhancement for a simple and universal detection of protein/small molecule interactions. RSC Adv 2018; 8:39913-39917. [PMID: 35558217 PMCID: PMC9091315 DOI: 10.1039/c8ra08515c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/19/2018] [Indexed: 12/04/2022] Open
Abstract
We herein describe a novel and efficient method for the detection of protein/small molecule (SM) interactions, which relies on the protein-induced fluorescence enhancement (PIFE). In this method, a duplex probe is designed to position Cy3 and SM at the optimal distance to maximize the effect of PIFE, which is utilized as the key component. In the presence of target proteins that bind to SM, the Cy3 is guided close to the target proteins, which significantly enhances the fluorescence signal through a process of PIFE. With this approach, we successfully analyzed a model target protein, streptavidin (STV) that interacts with biotin (BTN) in less than 10 min without any washing steps. In addition, the practical applicability of this method was demonstrated by reliably determining STV in human serum. Finally, the universal applicability of this method was demonstrated by monitoring the interaction between folate and folate receptors. We herein describe a novel and efficient method for the detection of protein/small molecule (SM) interactions, which relies on the protein-induced fluorescence enhancement (PIFE).![]()
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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18
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Mosayebi J, Kiyasatfar M, Laurent S. Synthesis, Functionalization, and Design of Magnetic Nanoparticles for Theranostic Applications. Adv Healthc Mater 2017; 6. [PMID: 28990364 DOI: 10.1002/adhm.201700306] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/14/2017] [Indexed: 12/13/2022]
Abstract
In order to translate nanotechnology into medical practice, magnetic nanoparticles (MNPs) have been presented as a class of non-invasive nanomaterials for numerous biomedical applications. In particular, MNPs have opened a door for simultaneous diagnosis and brisk treatment of diseases in the form of theranostic agents. This review highlights the recent advances in preparation and utilization of MNPs from the synthesis and functionalization steps to the final design consideration in evading the body immune system for therapeutic and diagnostic applications with addressing the most recent examples of the literature in each section. This study provides a conceptual framework of a wide range of synthetic routes classified mainly as wet chemistry, state-of-the-art microfluidic reactors, and biogenic routes, along with the most popular coating materials to stabilize resultant MNPs. Additionally, key aspects of prolonging the half-life of MNPs via overcoming the sequential biological barriers are covered through unraveling the biophysical interactions at the bio-nano interface and giving a set of criteria to efficiently modulate MNPs' physicochemical properties. Furthermore, concepts of passive and active targeting for successful cell internalization, by respectively exploiting the unique properties of cancers and novel targeting ligands are described in detail. Finally, this study extensively covers the recent developments in magnetic drug targeting and hyperthermia as therapeutic applications of MNPs. In addition, multi-modal imaging via fusion of magnetic resonance imaging, and also innovative magnetic particle imaging with other imaging techniques for early diagnosis of diseases are extensively provided.
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Affiliation(s)
- Jalal Mosayebi
- Department of Mechanical Engineering; Urmia University; Urmia 5756151818 Iran
| | - Mehdi Kiyasatfar
- Department of Mechanical Engineering; Urmia University; Urmia 5756151818 Iran
| | - Sophie Laurent
- Laboratory of NMR and Molecular Imaging; University of Mons; Mons Belgium
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19
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Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
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20
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DNA covalently linked to graphene oxide for biotin–streptavidin interaction assay. Talanta 2017; 163:140-145. [DOI: 10.1016/j.talanta.2016.10.096] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 11/17/2022]
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21
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Simple and convenient G-quadruplex-based fluorescent assay of biotin-streptavidin interaction via terminal protection of small molecule-linked DNA. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1980-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Detection of biotin-streptavidin interactions via terminal protection of small molecule linked DNA and the formation of fluorescent DNA-templated silver nanoclusters. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1968-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Denton KE, Krusemark CJ. Crosslinking of DNA-linked ligands to target proteins for enrichment from DNA-encoded libraries. MEDCHEMCOMM 2016; 7:2020-2027. [PMID: 28948007 PMCID: PMC5609701 DOI: 10.1039/c6md00288a] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Achieving sufficient enrichment of ligands from DNA-encoded libraries for detection can be difficult, particularly for low affinity ligands within highly complex libraries. To address this challenge, we present an approach for crosslinking DNA-linked ligands to target proteins using electrophilic or photoreactive groups. The approach involves the teathering of a ssDNA oligonucleotide to a DNA-encoded molecule to enable attachment of a reactive group post-synthetically via DNA hybridization. Crosslinking traps ligand-protein complexes while in solution and allows for stringent washing conditions to be applied in the subsequent purification. Five reactive groups (tosyl, NHS ester, sulfonyl fluoride, phenyl azide, and diazirine) were tested for crosslinking efficiency and specificity with three DNA-linked ligands to their target proteins. In a model selection, crosslinking resulted in improved enrichment of both high and a low affinity ligands in comparison to a selection with a solid-phase immobilized protein.
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Affiliation(s)
- Kyle E Denton
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Dr., West Lafayette, IN, USA 47906
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Dr., West Lafayette, IN, USA 47906
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24
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Carvalho SM, Mansur HS, Ramanery FP, Mansur AAP, Lobato ZIP, Leite MF. Cytotoxicity investigation of luminescent nanohybrids based on chitosan and carboxymethyl chitosan conjugated with Bi 2S 3 quantum dots for biomedical applications. Toxicol Res (Camb) 2016; 5:1017-1028. [PMID: 30090409 PMCID: PMC6062294 DOI: 10.1039/c6tx00039h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/13/2016] [Indexed: 11/21/2022] Open
Abstract
Bioengineered hybrids are emerging as a new class of nanomaterials consisting of a biopolymer and inorganic semiconductors used in biomedical and environmental applications. The aim of the present work was to determine the cytocompatibility of novel water-soluble Bi2S3 quantum dots (QDs) functionalized with chitosan and O-carboxymethyl chitosan (CMC) as capping ligands using an eco-friendly aqueous process at room temperature. These hybrid nanocomposites were tested for cytocompatibility using a 3-(4,5-dimethylthiazol-2yl) 2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay with cultured human osteosarcoma cells (SAOS), human embryonic kidney cells (HEK293T cells) and a LIVE/DEAD® viability-cytotoxicity assay. The results of the in vitro assays demonstrated that the CMC and chitosan-based nanohybrids were not cytotoxic and exhibited suitable cell viability responses. However, despite the "safe by design" approach used in this research, we have proved that the impact of the size, surface charge and biofunctionalization of the nanohybrids on cytotoxicity was cell type-dependent due to complex mechanisms. Thus, these novel bionanocomposites offer promising prospects for potential biomedical and pharmaceutical applications as fluorescent nanoprobes.
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Affiliation(s)
- Sandhra M Carvalho
- Center of Nanoscience , Nanotechnology and Innovation - CeNano2I , Department of Metallurgical and Materials Engineering , Federal University of Minas Gerais-UFMG , Brazil . ; ; Tel: +55-31-34091843
| | - Herman S Mansur
- Center of Nanoscience , Nanotechnology and Innovation - CeNano2I , Department of Metallurgical and Materials Engineering , Federal University of Minas Gerais-UFMG , Brazil . ; ; Tel: +55-31-34091843
| | - Fábio P Ramanery
- Center of Nanoscience , Nanotechnology and Innovation - CeNano2I , Department of Metallurgical and Materials Engineering , Federal University of Minas Gerais-UFMG , Brazil . ; ; Tel: +55-31-34091843
| | - Alexandra A P Mansur
- Center of Nanoscience , Nanotechnology and Innovation - CeNano2I , Department of Metallurgical and Materials Engineering , Federal University of Minas Gerais-UFMG , Brazil . ; ; Tel: +55-31-34091843
| | - Zelia I P Lobato
- Department of Preventive Veterinary Medicine , Federal University of Minas Gerais , Brazil
| | - Maria F Leite
- Department of Biochemistry and Immunology , Federal University of Minas Gerais , Brazil
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25
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Chen J, Liu Y, Ji X, He Z. Target-protecting dumbbell molecular probe against exonucleases digestion for sensitive detection of ATP and streptavidin. Biosens Bioelectron 2016; 83:221-8. [PMID: 27131994 DOI: 10.1016/j.bios.2016.04.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/03/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
In this work, a versatile dumbbell molecular (DM) probe was designed and employed in the sensitively homogeneous bioassay. In the presence of target molecule, the DM probe was protected from the digestion of exonucleases. Subsequently, the protected DM probe specifically bound to the intercalation dye and resulted in obvious fluorescence signal which was used to determine the target molecule in return. This design allows specific and versatile detection of diverse targets with easy operation and no sophisticated fluorescence labeling. Integrating the idea of target-protecting DM probe with adenosine triphosphate (ATP) involved ligation reaction, the DM probe with 5'-end phosphorylation was successfully constructed for ATP detection, and the limitation of detection was found to be 4.8 pM. Thanks to its excellent selectivity and sensitivity, this sensing strategy was used to detect ATP spiked in human serum as well as cellular ATP. Moreover, the proposed strategy was also applied in the visual detection of ATP in droplet-based microfluidic platform with satisfactory results. Similarly, combining the principle of target-protecting DM probe with streptavidin (SA)-biotin interaction, the DM probe with 3'-end biotinylation was developed for selective and sensitive SA determination, which demonstrated the robustness and versatility of this design.
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Affiliation(s)
- Jinyang Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yucheng Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
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26
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Torres Andón F, Alonso MJ. Nanomedicine and cancer immunotherapy – targeting immunosuppressive cells. J Drug Target 2015; 23:656-71. [DOI: 10.3109/1061186x.2015.1073295] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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27
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Xu H, Ma H, Yang P, Zhang X, Wu X, Yin W, Wang H, Xu D. Targeted polymer-drug conjugates: Current progress and future perspective. Colloids Surf B Biointerfaces 2015; 136:729-34. [PMID: 26513756 DOI: 10.1016/j.colsurfb.2015.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Abstract
The combination of polymer technology and targeted drug delivery may pave the way for more effective yet safer therapeutic options for cancer therapy. Polymer-drug conjugates belonging to polymer therapeutics represent an emerging approach for drug delivery. The development of smart targeted polymer-drug conjugates that can specifically deliver drugs at a sustained rate to tumor cells may substantially improve the therapeutic index of anticancer agents. In this update, we provide an overview of the most important targeting molecules, and systemically summarize the recent advances in the development of tumor-targeted polymer-drug conjugates. Additionally, several promising approaches for the future will also be presented.
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Affiliation(s)
- Hongyan Xu
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
| | - Haifeng Ma
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China.
| | - Peimin Yang
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
| | - Xia Zhang
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
| | - Xiangxia Wu
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
| | - Weidong Yin
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
| | - Hui Wang
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
| | - Dongmei Xu
- Department of pharmacy, People's Hospital of Linzi District, Linzi, Shandong Province 255400, China
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28
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Bao J, Krylova SM, Cherney LT, Hale RL, Belyanskaya SL, Chiu CH, Arico-Muendel CC, Krylov SN. Prediction of Protein–DNA Complex Mobility in Gel-Free Capillary Electrophoresis. Anal Chem 2015; 87:2474-9. [DOI: 10.1021/ac504504c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jiayin Bao
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Leonid T. Cherney
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Robert L. Hale
- GlaxoSmithKline, 343 Winter Street, Waltham, Mississippi 02451-8714, United States
| | | | - Cynthia H. Chiu
- GlaxoSmithKline, 343 Winter Street, Waltham, Mississippi 02451-8714, United States
| | | | - Sergey N. Krylov
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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29
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Gong X, Zhou W, Chai Y, Xiang Y, Yuan R. Terminal protection of small molecule-linked ssDNA for label-free and highly sensitive colorimetric detection of folate receptor biomarkers. RSC Adv 2015. [DOI: 10.1039/c4ra13997f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Protection of ssDNA from digesting by Exo I generates amplified color transition for label-free and sensitive detection of folate receptors.
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Affiliation(s)
- Xue Gong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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30
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Zhu Y, Wang G, Sha L, Qiu Y, Jiang H, Zhang X. A ratiometric colorimetric detection of the folate receptor based on terminal protection of small-molecule-linked DNA. Analyst 2015; 140:1260-4. [DOI: 10.1039/c4an02115k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Development of strategies for the sensitive and selective detection of the folate receptor (FR) that are simple and low cost is of great importance for assessing cancer therapeutics due to its crucial role in physiological, pharmacological and pathological processes.
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Affiliation(s)
- Yanhong Zhu
- Anhui Key Laboratory of Chem-Biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechnology
- Anhui Normal University
- Wuhu
| | - Guangfeng Wang
- Anhui Key Laboratory of Chem-Biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechnology
- Anhui Normal University
- Wuhu
| | - Liang Sha
- Anhui Key Laboratory of Chem-Biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechnology
- Anhui Normal University
- Wuhu
| | - Yuwei Qiu
- Anhui Key Laboratory of Chem-Biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechnology
- Anhui Normal University
- Wuhu
| | - Hong Jiang
- Anhui Key Laboratory of Chem-Biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechnology
- Anhui Normal University
- Wuhu
| | - Xiaojun Zhang
- Anhui Key Laboratory of Chem-Biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechnology
- Anhui Normal University
- Wuhu
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31
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Wang LJ, Zhang Y, Zhang CY. A target-triggered exponential amplification-based DNAzyme biosensor for ultrasensitive detection of folate receptors. Chem Commun (Camb) 2014; 50:15393-6. [DOI: 10.1039/c4cc07230h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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32
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Goodwin AP, Nakatsuka MA, Mattrey RF. Stimulus-responsive ultrasound contrast agents for clinical imaging: motivations, demonstrations, and future directions. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:111-23. [PMID: 25195785 DOI: 10.1002/wnan.1285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/23/2014] [Accepted: 07/06/2014] [Indexed: 12/17/2022]
Abstract
Microbubble ultrasound contrast agents allow imaging of the vasculature with excellent resolution and signal-to-noise ratios. Contrast in microbubbles derives from their interaction with an ultrasound wave to generate signal at harmonic frequencies of the stimulating pulse; subtracting the elastic echo caused by the surrounding tissue can enhance the specificity of these harmonic signals significantly. The nonlinear acoustic emission is caused by pressure-driven microbubble size fluctuations, which in both theoretical descriptions and empirical measurements was found to depend on the mechanical properties of the shell that encapsulates the microbubble as well as stabilizes it against the surrounding aqueous environment. Thus biochemically induced switching between a rigid 'off' state and a flexible 'on' state provides a mechanism for sensing chemical markers for disease. In our research, we coupled DNA oligonucleotides to a stabilizing lipid monolayer to modulate stiffness of the shell and thereby induce stimulus-responsive behavior. In initial proof-of-principle studies, it was found that signal modulation came primarily from DNA crosslinks preventing the microbubble size oscillations rather than merely damping the signal. Next, these microbubbles were redesigned to include an aptamer sequence in the crosslinking strand, which not only allowed the sensing of the clotting enzyme thrombin but also provided a general strategy for sensing other soluble biomarkers in the bloodstream. Finally, the thrombin-sensitive microbubbles were validated in a rabbit model, presenting the first example of an ultrasound contrast agent that could differentiate between active and inactive clots for the diagnosis of deep venous thrombosis.
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Affiliation(s)
- Andrew P Goodwin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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33
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Zhong Y, Meng F, Deng C, Zhong Z. Ligand-Directed Active Tumor-Targeting Polymeric Nanoparticles for Cancer Chemotherapy. Biomacromolecules 2014; 15:1955-69. [DOI: 10.1021/bm5003009] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yinan Zhong
- Biomedical Polymers Laboratory,
and Jiangsu Key Laboratory of Advanced Functional Polymer Design and
Application, College of Chemistry, Chemical Engineering and Materials
Science, Soochow University, Suzhou, 215123, People’s Republic of China
| | - Fenghua Meng
- Biomedical Polymers Laboratory,
and Jiangsu Key Laboratory of Advanced Functional Polymer Design and
Application, College of Chemistry, Chemical Engineering and Materials
Science, Soochow University, Suzhou, 215123, People’s Republic of China
| | - Chao Deng
- Biomedical Polymers Laboratory,
and Jiangsu Key Laboratory of Advanced Functional Polymer Design and
Application, College of Chemistry, Chemical Engineering and Materials
Science, Soochow University, Suzhou, 215123, People’s Republic of China
| | - Zhiyuan Zhong
- Biomedical Polymers Laboratory,
and Jiangsu Key Laboratory of Advanced Functional Polymer Design and
Application, College of Chemistry, Chemical Engineering and Materials
Science, Soochow University, Suzhou, 215123, People’s Republic of China
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34
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Terminal protection of small molecule-linked ssDNA-SWNT nanoassembly for sensitive detection of small molecule and protein interaction. CHINESE CHEM LETT 2013. [DOI: 10.1016/j.cclet.2013.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Ou LJ, Wang HB, Chu X. Terminal protection of small-molecule-linked DNA for sensitive fluorescence detection of protein binding based on nucleic acid amplification. Analyst 2013; 138:7218-23. [DOI: 10.1039/c3an01393f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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36
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Norris V, Thierry A, Amar P, Holland IB, Molina F. The mimic chain reaction. J Mol Microbiol Biotechnol 2012; 22:335-43. [PMID: 23221677 DOI: 10.1159/000345328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
It is sometimes speculated that the equivalent of the polymerase chain reaction might be developed for identification of peptides, proteins or other molecules. In general, though, it is believed that there can be no way to amplify targets such as proteins. Natural amplification systems do, however, exist as in the case of certain autoinducer systems in bacteria. Here, we outline a possible, generic method, the mimic chain reaction, for obtaining peptides with 3-D structures that mimic the 3-D structure of their targets. These targets would include a variety of molecules, including proteins. There are therefore two categories of applications: the ability via amplification firstly to detect a known protein or other target at an extremely low concentration, and secondly to obtain a set of peptides that mimic the structure of an unknown target and that can be used to obtain a 'photofit'.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, EA 3829, University of Rouen, Mont-Saint-Aignan, France.
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37
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Berezovski MV, Mironov GG. Utility of kinetic capillary electrophoresis-mass spectrometry to study protein dynamics and affinity interactions. Expert Rev Proteomics 2012. [PMID: 23194262 DOI: 10.1586/epr.12.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bao J, Krylov SN. Volatile kinetic capillary electrophoresis for studies of protein-small molecule interactions. Anal Chem 2012; 84:6944-7. [PMID: 22823518 DOI: 10.1021/ac301829t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kinetic capillary electrophoresis (KCE) is a toolset of homogeneous affinity methods for studying kinetics of noncovalent binding. Sensitive KCE measurements are typically done with fluorescence detection and require a fluorescent label on a smaller-sized binding partner. KCE with fluorescence detection is difficult to use for study of protein-small molecule interactions since labeling small molecules is cumbersome and can affect binding. A combination of KCE with mass-spectrometry (KCE-MS) has been recently suggested for label-free studies of protein-small molecule interactions. The major obstacle for studies by KCE-MS is a buffer mismatch between KCE and MS; MS requires volatile buffers while KCE of protein-ligand interactions is always run in near-physiological buffers. Here we asked a simple question: can protein-ligand interactions be studied with KCE in a volatile buffer? We compared three volatile buffers (ammonium acetate, ammonium bicarbonate, and ammonium formate) with a near-physiological buffer (Tris-acetate) for three protein-ligand pairs. The volatile buffers were found not to significantly affect protein-ligand complex stability; moreover, when used as CE run buffers, they facilitated good-quality separation of free ligands from the protein-ligand complexes. The use of volatile buffers instead of Tris-acetate in detection of small molecules by MS improved the detection limit by approximately 2 orders of magnitude. These findings prove the principle of "volatile" KCE, which can be easily coupled with MS to facilitate label-free kinetic studies of protein-small molecule interactions.
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Affiliation(s)
- Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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Mironov GG, Logie J, Okhonin V, Renaud JB, Mayer PM, Berezovski MV. Comparative study of three methods for affinity measurements: capillary electrophoresis coupled with UV detection and mass spectrometry, and direct infusion mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1232-1240. [PMID: 22544663 DOI: 10.1007/s13361-012-0386-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/23/2012] [Accepted: 03/23/2012] [Indexed: 05/31/2023]
Abstract
We present affinity capillary electrophoresis and mass spectrometry (ACE-MS) as a comprehensive separation technique for label-free solution-based affinity analysis. The application of ACE-MS for measuring affinity constants between eight small molecule drugs [ibuprofen, s-flurbiprofen, diclofenac, phenylbutazone, naproxen, folic acid, resveratrol, and 4,4'-(propane-1,3-diyl) dibenzoic acid] and β-cyclodextrin is described. We couple on-line ACE with MS to combine the separation and kinetic capability of ACE together with the molecular weight and structural elucidation of MS in one system. To understand the full potential of ACE-MS, we compare it with two other methods: Direct infusion mass spectrometry (DIMS) and ACE with UV detection (ACE-UV). After the evaluation, DIMS provides less reliable equilibrium dissociation constants than separation-based ACE-UV and ACE-MS, and cannot be used solely for the study of noncovalent interactions. ACE-MS determines apparent dissociation constants for all reacting small molecules in a mixture, even in cases when drugs overlap with each other during separation. The ability of ACE-MS to interact, separate, and rapidly scan through m/z can facilitate the simultaneous affinity analysis of multiple interacting pairs, potentially leading to the high-throughput screening of drug candidates.
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Affiliation(s)
- Gleb G Mironov
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada, K1N 6N5
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40
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Yangyuoru PM, Dhakal S, Yu Z, Koirala D, Mwongela SM, Mao H. Single-molecule measurements of the binding between small molecules and DNA aptamers. Anal Chem 2012; 84:5298-303. [PMID: 22702719 DOI: 10.1021/ac300427d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aptamers that bind small molecules can serve as basic biosensing platforms. Evaluation of the binding constant between an aptamer and a small molecule helps to determine the effectiveness of the aptamer-based sensors. Binding constants are often measured by a series of experiments with varying ligand or aptamer concentrations. Such experiments are time-consuming, material nonprudent, and prone to low reproducibility. Here, we use laser tweezers to determine the dissociation constant for aptamer-ligand interactions at the single-molecule level from only one ligand concentration. Using an adenosine 5'-triphosphate disodium salt (ATP) binding aptamer as an example, we have observed that the mechanical stabilities of aptamers bound with ATP are higher than those without a ligand. Comparison of the change in free energy of unfolding (ΔG(unfold)) between these two aptamers yields a ΔG of 33 ± 4 kJ/mol for the binding. By applying a Hess-like cycle at room temperature, we obtained a dissociation constant (K(d)) of 2.0 ± 0.2 μM, a value consistent with the K(d) obtained from our equilibrated capillary electrophoresis (CE) (2.4 ± 0.4 μM) and close to that determined by affinity chromatography in the literature (6 ± 3 μM). We anticipate that our laser tweezers and CE methodologies may be used to more conveniently evaluate the binding between receptors and ligands and also serve as analytical tools for force-based biosensing.
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Affiliation(s)
- Philip M Yangyuoru
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA
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41
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Krylova SM, Koshkin V, Bagg E, Schofield CJ, Krylov SN. Mechanistic studies on the application of DNA aptamers as inhibitors of 2-oxoglutarate-dependent oxygenases. J Med Chem 2012; 55:3546-52. [PMID: 22471443 PMCID: PMC4681096 DOI: 10.1021/jm300243h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli (E. coli) AlkB protein and its functional human homologues belong to a subfamily of 2-oxoglutarate (2OG) dependent oxygenases (2OG oxygenases for simplicity) that enable the repair of cytotoxic methylation damage in nucleic acids and that catalyze t-RNA oxidations. DNA alkylation is a major mechanism of action for cytotoxic anticancer drugs. Thus, the inhibition of oxidative demethylation, catalyzed by these enzymes, has the potential to improve the efficacy of chemotherapies. Here we report that oligonucleotide aptamers constitute a new class of potent inhibitors of 2OG oxygenases. DNA aptamers can selectively bind to AlkB, with nanomolar affinity, and efficiently inhibit catalysis. The mechanism of inhibition was studied by capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. Inhibition constants of the aptamers were determined and shown to correlate well with K(d) values. The results of kinetic analyses imply that the aptamers bind AlkB away from the active site. Our findings should stimulate the development of oligonucleotide aptamers for human homologues of AlkB and further their study as potential enhancers of chemotherapy efficiency.
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Affiliation(s)
- Svetlana M. Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Vasilij Koshkin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Eleanor Bagg
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
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Kamaly N, Xiao Z, Valencia PM, Radovic-Moreno AF, Farokhzad OC. Targeted polymeric therapeutic nanoparticles: design, development and clinical translation. Chem Soc Rev 2012; 41:2971-3010. [PMID: 22388185 PMCID: PMC3684255 DOI: 10.1039/c2cs15344k] [Citation(s) in RCA: 1133] [Impact Index Per Article: 94.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polymeric materials have been used in a range of pharmaceutical and biotechnology products for more than 40 years. These materials have evolved from their earlier use as biodegradable products such as resorbable sutures, orthopaedic implants, macroscale and microscale drug delivery systems such as microparticles and wafers used as controlled drug release depots, to multifunctional nanoparticles (NPs) capable of targeting, and controlled release of therapeutic and diagnostic agents. These newer generations of targeted and controlled release polymeric NPs are now engineered to navigate the complex in vivo environment, and incorporate functionalities for achieving target specificity, control of drug concentration and exposure kinetics at the tissue, cell, and subcellular levels. Indeed this optimization of drug pharmacology as aided by careful design of multifunctional NPs can lead to improved drug safety and efficacy, and may be complimentary to drug enhancements that are traditionally achieved by medicinal chemistry. In this regard, polymeric NPs have the potential to result in a highly differentiated new class of therapeutics, distinct from the original active drugs used in their composition, and distinct from first generation NPs that largely facilitated drug formulation. A greater flexibility in the design of drug molecules themselves may also be facilitated following their incorporation into NPs, as drug properties (solubility, metabolism, plasma binding, biodistribution, target tissue accumulation) will no longer be constrained to the same extent by drug chemical composition, but also become in-part the function of the physicochemical properties of the NP. The combination of optimally designed drugs with optimally engineered polymeric NPs opens up the possibility of improved clinical outcomes that may not be achievable with the administration of drugs in their conventional form. In this critical review, we aim to provide insights into the design and development of targeted polymeric NPs and to highlight the challenges associated with the engineering of this novel class of therapeutics, including considerations of NP design optimization, development and biophysicochemical properties. Additionally, we highlight some recent examples from the literature, which demonstrate current trends and novel concepts in both the design and utility of targeted polymeric NPs (444 references).
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Affiliation(s)
- Nazila Kamaly
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zeyu Xiao
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pedro M. Valencia
- The David H. Koch Institute for Integrative Cancer Research and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aleksandar F. Radovic-Moreno
- The David H. Koch Institute for Integrative Cancer Research and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Omid C. Farokhzad
- Laboratory of Nanomedicine and Biomaterials, Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Graphene and other nanomaterial-based electrochemical aptasensors. BIOSENSORS-BASEL 2012; 2:1-14. [PMID: 25585628 PMCID: PMC4263542 DOI: 10.3390/bios2010001] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 12/22/2011] [Accepted: 01/12/2012] [Indexed: 12/23/2022]
Abstract
Electrochemical aptasensors, which are based on the specificity of aptamer-target recognition, with electrochemical transduction for analytical purposes have received particular attention due to their high sensitivity and selectivity, simple instrumentation, as well as low production cost. Aptamers are functional nucleic acids with specific and high affinity to their targets, similar to antibodies. However, they are completely selected in vitro in contrast to antibodies. Due to their stability, easy chemical modifications and proneness to nanostructured device construction, aptamer-based sensors have been incorporated in a variety of applications including electrochemical sensing devices. In recent years, the performance of aptasensors has been augmented by incorporating novel nanomaterials in the preparation of better electrochemical sensors. In this review, we summarize the recent trends in the use of nanomaterials for developing electrochemical aptasensors.
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Wei X, Lin W, Ma N, Luo F, Lin Z, Guo L, Qiu B, Chen G. Sensitive fluorescence biosensor for folate receptor based on terminal protection of small-molecule-linked DNA. Chem Commun (Camb) 2012; 48:6184-6. [DOI: 10.1039/c2cc31979a] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Krylova SM, Dove PM, Kanoatov M, Krylov SN. Slow-dissociation and slow-recombination assumptions in nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem 2011; 83:7582-5. [PMID: 21853979 DOI: 10.1021/ac2018876] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a kinetic affinity method with both analytical and preparative applications. NECEEM requires that the dissociation of the complexes be negligible in its first phase and the recombination of the dissociated complexes be negligible in its second phase. Here, we introduce a method, which facilitates easy examination of whether or not these requirements are satisfied. We derived expressions for two parameters, termed the slow-dissociation parameter (SDP) and slow-recombination parameter (SRP), which can be used to assess the assumptions. Both parameters should be much less than 1 for the assumptions to be satisfied. We calculated the two parameters for new and previously published NECEEM experiments and found that the assumptions were satisfied in all of them. Finally, we discuss changes to NECEEM conditions that should be done if the assumptions are found not to be satisfied. The SDP/SRP assessment helps to easily validate the results of NECEEM-based analyses and thus makes the NECEEM method more robust.
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Affiliation(s)
- Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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46
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Özalp VC, Schäfer T. Aptamer-Based Switchable Nanovalves for Stimuli-Responsive Drug Delivery. Chemistry 2011; 17:9893-6. [DOI: 10.1002/chem.201101403] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Indexed: 11/10/2022]
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47
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de Jong S, Krylov SN. Protein labeling enhances aptamer selection by methods of kinetic capillary electrophoresis. Anal Chem 2011; 83:6330-5. [PMID: 21728308 DOI: 10.1021/ac201242r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methods of kinetic capillary electrophoresis (KCE) facilitate highly efficient selection of DNA aptamers for protein targets. The inability to detect native proteins at low concentrations in capillary electrophoresis creates, however, a significant obstacle for many important protein targets. Here we suggest that protein labeling with new Chromeo dyes can help to overcome this obstacle. By labeling a number of proteins with Chromeo P503, we show that the labeling procedure enables accurate detection of proteins in CE without significantly affecting their electrophoretic mobility or their ability to bind DNA. Moreover, Chromeo P503 does not appear to label the amino-groups of buffer components to a significant extent, making the labeling procedure compatible with a large number of selection and run buffers. Fluorescent labeling of protein targets with Chromeo dyes empowers selection of aptamers by KCE methods and promises to increase the rate at which aptamers for new targets are being developed and introduced in various applications.
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48
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Wu Z, Wang H, Guo M, Tang LJ, Yu RQ, Jiang JH. Terminal Protection of Small Molecule-Linked DNA: A Versatile Biosensor Platform for Protein Binding and Gene Typing Assay. Anal Chem 2011; 83:3104-11. [DOI: 10.1021/ac1033769] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhan Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Hongqi Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Min Guo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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Mironov GG, Okhonin V, Gorelsky SI, Berezovski MV. Revealing Equilibrium and Rate Constants of Weak and Fast Noncovalent Interactions. Anal Chem 2011; 83:2364-70. [DOI: 10.1021/ac200010u] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Gleb G. Mironov
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
| | - Victor Okhonin
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
| | - Serge I. Gorelsky
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie Curie, Ottawa, Canada K1N 6N5
| | - Maxim V. Berezovski
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5
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50
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Okhonin V, Berezovski MV, Krylov SN. MASKE: Macroscopic Approach to Studying Kinetics at Equilibrium. J Am Chem Soc 2010; 132:7062-8. [DOI: 10.1021/ja100104m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Victor Okhonin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Maxim V. Berezovski
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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