1
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Mili M, Bachu V, Kuri PR, Singh NK, Goswami P. Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications. Biophys Chem 2024; 309:107218. [PMID: 38547671 DOI: 10.1016/j.bpc.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/21/2024] [Accepted: 03/17/2024] [Indexed: 04/22/2024]
Abstract
Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.
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Affiliation(s)
- Malaya Mili
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Vinay Bachu
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Pooja Rani Kuri
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | | | - Pranab Goswami
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India.
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2
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Albright S, Cacace M, Tivon Y, Deiters A. Cell Surface Labeling and Detection of Protein Tyrosine Kinase 7 via Covalent Aptamers. J Am Chem Soc 2023; 145:16458-16463. [PMID: 37473438 PMCID: PMC10401710 DOI: 10.1021/jacs.3c02752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 07/22/2023]
Abstract
Covalent aptamers are novel biochemical tools for fast and selective transfer of labels to target proteins. Equipped with cleavable electrophiles, these nucleic acid probes enable the installation of functional handles onto native proteins. The high affinity and specificity with which aptamers bind their selected targets allows for quick, covalent labeling that can compete with nuclease-mediated degradation. Here, we introduce the first application of covalent aptamers to modify a specific cell surface protein through proximity-driven label transfer. We targeted protein tyrosine kinase 7 (PTK7), a prominent cancer marker, and demonstrated aptamer-mediated biotin transfer to specific lysine residues on the extracellular domain of the protein. This allowed for tracking of PTK7 expression, localization, and cellular internalization. These studies validate the programmability of covalent aptamers and highlight their applicability in a cellular context, including protein and small molecule delivery.
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Affiliation(s)
| | | | - Yaniv Tivon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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3
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Wang R, Wang X, Xie S, Zhang Y, Ji D, Zhang X, Cui C, Jiang J, Tan W. Molecular elements: novel approaches for molecular building. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220024. [PMID: 36633277 PMCID: PMC9835600 DOI: 10.1098/rstb.2022.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xueqiang Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Yanyan Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Dingkun Ji
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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4
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Pan J, Deng F, Zeng L, Liu Z, Chen J. Target-mediated competitive hybridization of hairpin probes for kanamycin detection based on exonuclease III cleavage and DNAzyme catalysis. Anal Bioanal Chem 2022; 414:8255-8261. [PMID: 36178489 DOI: 10.1007/s00216-022-04354-3] [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: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022]
Abstract
Based on aptamer recognition and target-mediated competitive hybridization of hairpin probes, we developed a fluorescence sensor for kanamycin (KAN) detection. The aptamer and KAN binding will open hairpin H1 to release the trigger DNA fragment, which can initiate the competitive hybridization between hairpins H2 and H3. Then, exonuclease III (Exo III) can cleave H2 and H3 to produce numerous DNA3 and DNA4. Through the synergetic hybridization among DNA1, DNA2, DNA3, and DNA4, an active Mg2+-DNAzyme can be formed. The cleavage reaction toward FAM-BHQ-modified DNA2 will produce a high fluorescence signal for KAN assay. Through Exo III-guided cleavage and Mg2+-DNAzyme-based catalysis, the sensor exhibits high sensitivity, with a detection limit of 3.1 fM. This method is robust and has been applied to the detection of KAN in milk and water samples with good accuracy and reliability. Our developed fluorescence sensor exhibits the advantages of simple operation, high sensitivity, and good robustness, which are beneficial for KAN detection in food samples.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Lingwen Zeng
- Guangdong Langyuan Biotechnology Co., LTD, Foshan, 528313, China
- School of Food Science and Engineering, Foshan University, Foshan, 528231, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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5
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Gilazieva Z, Ponomarev A, Rizvanov A, Solovyeva V. The Dual Role of Mesenchymal Stromal Cells and Their Extracellular Vesicles in Carcinogenesis. BIOLOGY 2022; 11:biology11060813. [PMID: 35741334 PMCID: PMC9220333 DOI: 10.3390/biology11060813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/07/2023]
Abstract
Simple Summary Extracellular vesicles (EVs) are membrane structures that play the role of intermediaries between tumor cells and the tumor microenvironment (TME) because they have the ability to transport lipids, transcription factors, mRNA, and proteins. Mesenchymal stem cells (MSCs) are a major component of the TME and may have different effects on tumor progression using EVs. This review includes information about various studies which have reported that EVs from MSCs can have either antitumor or pro-tumor effects, depending on both the tumor type and developmental stage. It provides an overview of the published data on EV MSCs and their effect on tumor cells. In addition, the use of EV MSCs for the development of new methods for treating oncological diseases is described. Abstract Mesenchymal stem cells (MSCs) are a major component of the tumor microenvironment (TME) and play an important role in tumor progression. MSCs remodel the extracellular matrix, participate in the epithelial–mesenchymal transition, promote the spread of metastases, and inhibit antitumor immune responses in the TME; however, there are also data pertaining to the antitumor effects of MSCs. MSCs activate the cell death mechanism by modulating the expression of proteins involved in the regulation of the cell cycle, angiogenesis receptors, and proapoptotic proteins. One of the main ways in which MSCs and TME interact is through the production of extracellular vesicles (EVs) by cells. Currently, data on the effects of both MSCs and their EVs on tumor cells are rather contradictory. Various studies have reported that EVs from MSCs can have either antitumor or pro-tumor effects, depending on both the tumor type and developmental stage. In this review, we discuss published data on EV MSCs and their effect on tumor cells. The molecular composition of vesicles obtained from MSCs is also presented in the review. In addition, the use of EV MSCs for the development of new methods for treating oncological diseases is described.
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6
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Murtaza G, Rizvi AS, Qiu L, Xue M, Meng Z. Aptamer empowered hydrogels: Fabrication and bio‐sensing applications. J Appl Polym Sci 2022. [DOI: 10.1002/app.52441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ghulam Murtaza
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing China
| | - Aysha Sarfraz Rizvi
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing China
| | - Lili Qiu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing China
| | - Min Xue
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing China
| | - Zihui Meng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing China
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7
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Yang C, Zhao H, Sun Y, Wang C, Geng X, Wang R, Tang L, Han D, Liu J, Tan W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3083-3095. [PMID: 35293579 PMCID: PMC8989545 DOI: 10.1093/nar/gkac156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/24/2022] [Accepted: 02/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Cheng Wang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xinyao Geng
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ruowen Wang
- To whom correspondence should be addressed. Tel: +86 02168385698; Fax:+86 02168385698;
| | - Lumin Tang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianjun Liu
- Correspondence may also be addressed to Jianjun Liu.
| | - Weihong Tan
- Correspondence may also be addressed to Weihong Tan.
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8
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Keijzer JF, Albada B. DNA-assisted site-selective protein modification. Biopolymers 2021; 113:e23483. [PMID: 34878181 PMCID: PMC9285461 DOI: 10.1002/bip.23483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/09/2022]
Abstract
Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
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9
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Yang W, Nan H, Xu Z, Huang Z, Chen S, Li J, Li J, Yang H. DNA-Templated Glycan Labeling for Monitoring Receptor Spatial Distribution in Living Cells. Anal Chem 2021; 93:12265-12272. [PMID: 34474560 DOI: 10.1021/acs.analchem.1c01815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tracking the spatial distribution of receptor tyrosine kinases in their native environment contributes to understanding the homeostatic or pathological states at a molecular level. Conjugation of DNA tags to a specific receptor is a powerful tool for monitoring receptor spatial distribution. However, long-term stable trafficking in live cells without interfering with the intrinsic receptor function remains a challenge. Here, we report a general DNA-templated glycan labeling strategy to track spatial distribution of a specific receptor in living cells. Different from existing target-selective covalent methods, the DNA tags were incorporated in glycan of a specific receptor via aptamer-assisted metabolic glycan labeling, thus resulting in minimal perturbation to the receptor's biological function. As proof of concept, covalent tagging of MET, HER2, and EGFR was achieved, and then the spatial distribution was successfully monitored, including homo-/heterodimerization and internalization. Overall, the proposed strategy will greatly aid in investigating receptor dynamics and is conducive to understanding their biological function in the native environment.
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Affiliation(s)
- Wen Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Hexin Nan
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Zhifei Xu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Zixiang Huang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Shan Chen
- Institute of Oceanography, Minjiang University, Fuzhou350108, Fujian, People's Republic of China
| | - Jingying Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China
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10
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Tivon Y, Falcone G, Deiters A. Protein Labeling and Crosslinking by Covalent Aptamers. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yaniv Tivon
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Gianna Falcone
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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11
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Tivon Y, Falcone G, Deiters A. Protein Labeling and Crosslinking by Covalent Aptamers. Angew Chem Int Ed Engl 2021; 60:15899-15904. [PMID: 33928724 PMCID: PMC8260448 DOI: 10.1002/anie.202101174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
We developed a new approach to selectively modify native proteins in their biological environment using electrophilic covalent aptamers. These aptamers are generated through introduction of a proximity-driven electrophile at specific nucleotide sites. Using thrombin as a proof-of-concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease-resistant enzyme inhibition.
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Affiliation(s)
- Yaniv Tivon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Gianna Falcone
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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12
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Wu L, Wang Y, Xu X, Liu Y, Lin B, Zhang M, Zhang J, Wan S, Yang C, Tan W. Aptamer-Based Detection of Circulating Targets for Precision Medicine. Chem Rev 2021; 121:12035-12105. [PMID: 33667075 DOI: 10.1021/acs.chemrev.0c01140] [Citation(s) in RCA: 220] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.
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Affiliation(s)
- Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yidi Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bingqian Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jialu Zhang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuang Wan
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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13
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Tan Y, Li Y, Qu YX, Su Y, Peng Y, Zhao Z, Fu T, Wang XQ, Tan W. Aptamer-Peptide Conjugates as Targeted Chemosensitizers for Breast Cancer Treatment. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9436-9444. [PMID: 33306339 DOI: 10.1021/acsami.0c18282] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
High levels of heat shock protein 70 (HSP70) in tumors are commonly associated with poor prognosis, enhanced doxorubicin (DOX)-induced cardiotoxicity, and even drug resistance in DOX-related cancer chemotherapy. Several peptides possess remarkable protein inhibition and chemosensitization effects, which are attributed to their specific targeting ability against HSP70. However, the inherent poor cell penetration capacity considerably restricts the biomedical applications of these peptides. We herein describe the design and development of anti-MUC1 aptamer-peptide conjugates (ApPCs) as targeted chemosensitizers to overcome the above-mentioned issues. Moreover, DOX could be loaded on the ApPC to deliver the DOX-enclosed agent ApPC-DOX, which simultaneously acts as a targeted chemosensitizer and anticancer agent for combating drug resistance in breast cancer therapy. This innovative, engineered biocompatible conjugate not only enhances the sensitivity of DOX-resistant cells but also alleviates cardiotoxicity of DOX in vivo, highlighting the success of this targeted chemosensitizer strategy.
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Affiliation(s)
- Yan Tan
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Yingying Li
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Yi-Xin Qu
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Yuanye Su
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Yongbo Peng
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Zilong Zhao
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Ting Fu
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Xue-Qiang Wang
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, P. R. China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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14
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Huang Y, Deng Y, Zhang J, Meng L, Li X. Direct ligand screening against membrane proteins on live cells enabled by DNA-programmed affinity labelling. Chem Commun (Camb) 2021; 57:3769-3772. [DOI: 10.1039/d1cc00961c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA-programmed affinity labelling (DPAL) enables the screening of chemical compounds against membrane proteins directly on live cells.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Yuqing Deng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Jianfu Zhang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Pokfulam Road
- Hong Kong SAR
- China
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15
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Huang Y, Meng L, Nie Q, Zhou Y, Chen L, Yang S, Fung YME, Li X, Huang C, Cao Y, Li Y, Li X. Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells. Nat Chem 2020; 13:77-88. [PMID: 33349694 DOI: 10.1038/s41557-020-00605-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 11/10/2020] [Indexed: 12/30/2022]
Abstract
Membrane proteins on the cell surface perform a myriad of biological functions; however, ligand discovery for membrane proteins is highly challenging, because a natural cellular environment is often necessary to maintain protein structure and function. DNA-encoded chemical libraries (DELs) have emerged as a powerful technology for ligand discovery, but they are mainly limited to purified proteins. Here we report a method that can specifically label membrane proteins with a DNA tag, and thereby enable target-specific DEL selections against endogenous membrane proteins on live cells without overexpression or any other genetic manipulation. We demonstrate the generality and performance of this method by screening a 30.42-million-compound DEL against the folate receptor, carbonic anhydrase 12 and the epidermal growth factor receptor on live cells, and identify and validate a series of novel ligands for these targets. Given the high therapeutic significance of membrane proteins and their intractability to traditional high-throughput screening approaches, this method has the potential to facilitate membrane-protein-based drug discovery by harnessing the power of DEL.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Langdong Chen
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Shilian Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yi Man Eva Fung
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaomeng Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Cen Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, Shanghai, China.
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK, Hong Kong SAR, China.
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16
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Liu L, Kuang Y, Wang Z, Chen Y. A photocleavable peptide-tagged mass probe for chemical mapping of epidermal growth factor receptor 2 (HER2) in human cancer cells. Chem Sci 2020; 11:11298-11306. [PMID: 34094372 PMCID: PMC8162480 DOI: 10.1039/d0sc04481d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/10/2020] [Indexed: 12/31/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) testing has great value for cancer diagnosis, prognosis and treatment selection. However, the clinical utility of HER2 is frequently tempered by the uncertainty regarding the accuracy of the methods currently available to assess HER2. The development of novel methods for accurate HER2 testing is in great demand. Considering the visualization features of in situ imaging and the quantitative capability of mass spectrometry, integration of the two components into a molecular mapping approach has attracted increasing interest. In this work, we reported an integrated chemical mapping approach using a photocleavable peptide-tagged mass probe for HER2 detection. The probe consists of four functional domains, including the recognition unit of an aptamer to catch HER2, a fluorescent dye moiety (FITC) for fluorescence imaging, a reporter peptide for mass spectrometric quantification, and a photocleavable linker for peptide release. After characterization of this novel probe (e.g., conjugation efficiency, binding affinity and specificity, and photolysis release efficiency), the probe binding and photolysis release conditions were optimized. Then, fluorescence images were collected, and the released reporter peptide after photolysis was quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A limit of quantification (LOQ) of 25 pM was obtained, which very well meets the requirements for clinical laboratory testing. Finally, the developed assay was applied for HER2 testing in four breast cancer cell lines and 42 pairs of human breast primary tumors and adjacent normal tissue samples. Overall, this integrated approach based on a photocleavable peptide-tagged mass probe can provide chemical mapping including both quantitative and visual information of HER2 reliably and consistently, and may pave the way for clinical applications in a more accurate manner.
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Affiliation(s)
- Liang Liu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University Wuhan 430071 China
| | - Yuqiong Kuang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- Department of Pharmacy, The First Affiliated Hospital with Nanjing Medical University 210029 China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- State Key Laboratory of Reproductive Medicine, Key Laboratory of Cardiovascular & Cerebrovascular Medicine Nanjing 210029 China
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17
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Pan X, Yang Y, Li L, Li X, Li Q, Cui C, Wang B, Kuai H, Jiang J, Tan W. A bispecific circular aptamer tethering a built-in universal molecular tag for functional protein delivery. Chem Sci 2020; 11:9648-9654. [PMID: 34123176 PMCID: PMC8161142 DOI: 10.1039/d0sc02279a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/19/2020] [Indexed: 01/12/2023] Open
Abstract
Chemically engineering endogenous amino acids with a molecular tag is one of the most common routes of artificially functionalizing proteins for identification or cellular delivery. However, it is challenging to make conjugation efficient, facile and productive as well as avoiding a high chance of deactivation of the functional proteins. Here we present a new and straightforward design to specifically tether the distinct six polyhistidine tag, terminally expressed on protein cargoes and cellular membrane proteins by using bispecific circular aptamers (bc-apts). The anti-His tag aptamer on one end of the bc-apt can easily recognize the biorthogonal six polyhistidine tag (His tag) on functional proteins like EGFP or RNase A. Meanwhile, a cell-specific aptamer, sgc8, on the other end efficiently facilitates the targeted delivery of functional proteins, improving their overall bioactivity in the cellular milieu by around 4 fold. Therefore, the nuclease-resistant bc-apt is a promising molecular tethering reagent to enable the noncovalent crosslink between live diseased cells and His tag protein cargoes.
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Affiliation(s)
- Xiaoshu Pan
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
| | - Yu Yang
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
| | - Long Li
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
| | - Xiaowei Li
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
| | - Qiang Li
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
| | - Cheng Cui
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 P. R. China
| | - Bang Wang
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 P. R. China
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 P. R. China
| | - Weihong Tan
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida Gainesville FL 32611-7200 USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 P. R. China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
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18
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020; 59:17525-17532. [DOI: 10.1002/anie.202001205] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/14/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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19
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Zhang J, Peng J, Huang Y, Meng L, Li Q, Xiong F, Li X. Identification of Histone deacetylase (HDAC)‐Associated Proteins with DNA‐Programmed Affinity Labeling. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Qingrong Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK Pokfulam Road Hong Kong SAR China
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20
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Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci 2020; 21:ijms21124522. [PMID: 32630547 PMCID: PMC7350236 DOI: 10.3390/ijms21124522] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.
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21
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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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22
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Kim W, Lee JS, Jang J. Aptamer-Functionalized Three-Dimensional Carbon Nanowebs for Ultrasensitive and Free-Standing PDGF Biosensor. ACS APPLIED MATERIALS & INTERFACES 2020; 12:20882-20890. [PMID: 32315526 DOI: 10.1021/acsami.0c03709] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Research on flexible biosensors is mostly focused on their use in obtaining information on physical signals (such as temperature, heart rate, pH, and intraocular pressure). Consequently, there are hardly any studies on using flexible electronics for detecting biomolecules and biomarkers that cause diseases. In this study, we propose a flexible, three-dimensional carbon nanoweb (3DCNW)-based aptamer sensor to detect the platelet-induced growth factor (PDGF), which is an oncogenic biomarker. As a template for the 3D structure, poly(acrylonitrile) (PAN) nanowebs were synthesized using a facile electrospinning process. The PAN nanowebs were then subjected to chemical vapor deposition with copper powder. This was followed by Cu etching to generate carbon protrusions on the web surface. As an active site, PDGF-B binding aptamer was introduced on the 3DCNW surface to form biosensor electrodes. The 3DCNW-based aptasensor exhibited excellent sensitivity (down to 1.78 fM), with high selectivity, reversibility, and stability to PDGF-BB.
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Affiliation(s)
- Wooyoung Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Jun Seop Lee
- Department of Materials Science and Engineering, Gachon University, 1342 Seongnam-Daero, Sujeong-Gu, Seongnam-Si, Gyeonggi-Do 13120, Republic of Korea
| | - Jyongsik Jang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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23
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Sun Y, Gao F, Yang C, Li Y, Jin C, Xie S, Lv C, Ding D, Han D, Li J, Wang R, Tan W. Construction of Bispecific Aptamer-Drug Conjugate by a Hybrid Chemical and Biological Approach. Bioconjug Chem 2020; 31:1289-1294. [PMID: 32223180 DOI: 10.1021/acs.bioconjchem.0c00071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bispecific aptamer-drug conjugates (BsApDC) may improve the efficacy of drugs by enhancing cellular internalization and targeted delivery. Nevertheless, the synthesis of single-molecular BsApDC has not yet been reported, and it could be thwarted by synthetic challenges. Herein we report a general approach to synthesize a BsApDC hybridized chemical and biological method. Primers incorporated with 5-Fluorouracil (5-FU), 10-Hydroxycamptothecin, and Maleimidocaproyl-valine-citrulline-p-aminobenzoyloxycarbonyl-monomethyl auristatin E(vcMMAE) were prepared by chemical synthesis, which were converted to corresponding ApDCs efficiently by enzymatic reaction. Biological studies revealed that BsApDC binds with target cells with enhanced internalization and better inhibitory activity, demonstrating the potential of BsApDCs for targeted tumor therapy.
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Affiliation(s)
- Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Fei Gao
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Cai Yang
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Yingying Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan 410082, China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan 410082, China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan 410082, China
| | - Cheng Lv
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Ding Ding
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Juan Li
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240, China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan 410082, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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24
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Su L, Chen T, Xue T, Sheng A, Cheng L, Zhang J. Fabrication of pH-Adjusted Boronic Acid-Aptamer Conjugate for Electrochemical Analysis of Conjugated N-Glycolylneuraminic Acid. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7650-7657. [PMID: 31951374 DOI: 10.1021/acsami.9b23029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, the boronic acid-aptamer conjugate (BAAC) is elaborately designed and explored as a recognition unit. The admirable properties of the pH-dependent boronic acid ester are integrated with the specific capturing capability of the modified aptamer; thus, BAAC can efficiently and selectively bind with the target by adjusting the pH values. An electrochemical biosensor based on pH-adjusted BAAC has been further developed for the analysis of CNeu5Gc, an important biomarker of different kinds of cancer. The boronic acid moiety in BAAC can react with CNeu5Gc to form a BAAC-CNeu5Gc complex under acidic conditions, followed by the release of CNeu5Gc from the complex and subsequent capture by the aptamer moiety with the adjustment of the pH value to alkalinity. With simplicity, high specificity, and efficiency, the biosensor exhibits a wide linear range from 2.816 to 3603.960 ng/mL with a low detection limit of 1.224 ng/mL and can be applied to analyze CNeu5Gc in animal food samples. Besides, this work can also provide a kind of modified aptamer, i.e., the chemical capturing group-modified aptamer, to give a new viewpoint for the exploration of other functionalized aptamers.
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Affiliation(s)
- Lihong Su
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Tingjun Chen
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Tianxiang Xue
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Anzhi Sheng
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
- Shanghai Key Laboratory of Bio-Energy Crops , Shanghai University , Shanghai 200444 , P. R. China
| | - Liangfen Cheng
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
| | - Juan Zhang
- Laboratory of Biosensing Technology, School of Life Sciences , Shanghai University , Shanghai 200444 , P. R. China
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26
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Li L, Han B, Wang Y, Zhao J, Cao Y. Simple and universal signal labeling of cell surface for amplified detection of cancer cells via mild reduction. Biosens Bioelectron 2019; 145:111714. [PMID: 31546202 DOI: 10.1016/j.bios.2019.111714] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 01/08/2023]
Abstract
Membrane protein, a novel surface biomarker, plays an important role in cell recognition and disease diagnosis. Accurate recognition of membrane protein ensure high specificity of cell identification, while introducing signal molecules onto cell membrane is critical to achieve high sensitivity. In this work, we introduced a simple and universal signal labeling approach for cancer cell detection based on mild reduction-mediated cell engineering. This approach included the mild reduction of disulfide bonds within membrane proteins and the introduction of DNA bridge complex-templated silver nanoclusters (DNA bridge-AgNCs) through the thiol-maleimide conjugation. The mild reduction reactions on the cell surface significantly increased the binding sites for signal labeling, and DNA bridge-AgNCs served as a scaffold of signal amplification, resulting in a wide linear range from 50-2 × 106 cells, and a detection limit of 15 cells. In addition, the method also showed good selectivity in complex environment. Therefore, this method may have great application space in the field of cell detection and even disease diagnosis in the near future.
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Affiliation(s)
- Lingling Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China; Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University, 200444, PR China
| | - Bing Han
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Ying Wang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
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27
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Skovsgaard MB, Mortensen MR, Palmfeldt J, Gothelf KV. Aptamer-Directed Conjugation of DNA to Therapeutic Antibodies. Bioconjug Chem 2019; 30:2127-2135. [PMID: 31247138 DOI: 10.1021/acs.bioconjchem.9b00363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A method for aptamer directed conjugation of DNA to therapeutic antibodies has been developed. In the method, an antibody selective aptamer binds to a specific site in the constant domain of human IgG1 antibodies and is used for both templated and direct conjugation to the antibodies. Through optimization of the design and reaction conditions, the antibody-DNA conjugates could be produced efficiently using equal stoichiometry of protein and DNA. Three different antibodies were evaluated, and the conjugates were characterized by anion exchange chromatography and SDS-PAGE. The conjugation sites for one of the antibodies were determined by MS/MS analysis of the digested conjugate. The antibody-DNA conjugate was also tested for receptor binding on cell surfaces showing retained binding.
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Affiliation(s)
- Mikkel B Skovsgaard
- iNANO, Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C, Denmark
| | - Michael R Mortensen
- iNANO, Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C, Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine , Aarhus University , Palle Juul-Jensens Boulevard 99 , DK-8200 Aarhus N, Denmark
| | - Kurt V Gothelf
- iNANO, Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C, Denmark
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28
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Pant P, Jayaram B. C5' omitted DNA enhances bendability and protein binding. Biochem Biophys Res Commun 2019; 514:979-984. [PMID: 31092333 DOI: 10.1016/j.bbrc.2019.05.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 12/24/2022]
Abstract
Protein-DNA interactions are of great biological importance. The specificity and strength of these intimate contacts are crucial in the proper functioning of a cell, wherein the role of DNA dynamic bendability has been a matter of discussion. We relate DNA bendability to protein binding by introducing some simple modifications in the DNA structure. We removed C5' carbon in first modified structure and the second has an additional carbon between C3' and 3'-OH, hereby pronounced as C(-) and C(+) nucleic acids respectively. We observed that C(+) nucleic acid retains B-DNA duplex as seen by means of 500 ns long molecular dynamics (MD) simulations, structural and energetic calculations, while C(-) nucleic acid attains a highly bend structure. We transferred these observations to a protein-DNA system in order to monitor as to what extent the bendability enhances the protein binding. The energetics of binding is explored by performing 100 ns long MD simulations on control and modified DNA-protein complexes followed by running MM-PBSA/GBSA calculations on the resultant structures. It is observed that C(+) nucleic acid has protein binding in close correspondence to the control system (∼-14 kcal/mol) due to their relatable structure, while the C(-) nucleic acid displayed high binding to the protein (∼-18 kcal/mol). DelPhi based calculations reveal that the high binding could be the result of enhanced electrostatic interactions caused by exposed bases in the bend structure for protein recognition. Such modified oligonucleotides, due to their improved binding to protein and resistance to nuclease degradation, have a great therapeutic value.
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Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, 110016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, 110016, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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29
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Jiang Y, Tang Y, Miao P. Polydopamine nanosphere@silver nanoclusters for fluorescence detection of multiplex tumor markers. NANOSCALE 2019; 11:8119-8123. [PMID: 30994693 DOI: 10.1039/c9nr01307e] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
There is an increasing demand to establish a convenient and stable analytical methodology for screening multiplex tumor markers in early diagnosis of cancers. In this work, an innovative fluorescence method is proposed for simultaneous detection of alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA). A polydopamine nanosphere@silver nanocluster (PDAN@AgNC) system is introduced for fluorescence quenching and recovery. The AgNCs with different emissions are synthesized using different DNA templates, which also contain aptamer sequences towards AFP and CEA, respectively. These single-stranded DNA sequences could be adsorbed on the surface of the PDAN through π-π stacking, which results in the quenching of AgNCs. However, in the presence of the corresponding tumor marker, the aptamer/target complex forms which releases AgNCs from the surface of the PDAN and the recovered fluorescence could be used to indicate the concentration of the tumor marker. This PDAN@AgNC system has been validated preliminarily to screen human serum samples with excellent results. Taking advantages of simplicity, enzyme/antibody-free nature, low cost and convenient operation, the proposed biosensor has great potential to be used in biomedical research studies and clinical diagnosis.
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Affiliation(s)
- Yiting Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China.
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30
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Xiong H, Yan J, Cai S, He Q, Peng D, Liu Z, Liu Y. Cancer protein biomarker discovery based on nucleic acid aptamers. Int J Biol Macromol 2019; 132:190-202. [PMID: 30926499 DOI: 10.1016/j.ijbiomac.2019.03.165] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/22/2019] [Accepted: 03/24/2019] [Indexed: 01/11/2023]
Abstract
Identification of biomarkers is essential for diagnosis, targeted therapy and prognosis evaluation of diseases, especially cancers. Currently, the number of ideal clinical biomarkers is still limited partially because of lacking efficient methods in biomarker discovery. Nucleic acid aptamers are artificial single-stranded DNA or RNA sequences that can selectively bind to various targets with high specificity and affinity. Moreover, aptamers possess desirable advantages, including easy synthesis, convenient modification, relative chemical stability and low immunogenicity. Recently, different aptamer-based strategies have been developed to facilitate the discovery of biomarkers. Based on cell-SELEX technology, the selected aptamers can be used to identify cell-surface protein biomarkers of different cancer cells. SOMAscan can analyze thousands of proteins of different biological samples, which becomes a multiplexed protein biomarker discovery platform. Additionally, secreted protein biomarkers can be discovered by aptamers screened through secretome SELEX. In order to facilitate the identification of target proteins, several covalent cross-linking strategies have been developed, such as aptamer-based affinity labeling (ABAL), DNA-templated aptamer and protein-aptamer template (PAT). In this review, we mainly highlight the emerging nucleic acid aptamer-based biomarker discovery strategies and demonstrate their unique technological advantages in discovering cancer biomarkers. The challenges and perspectives of aptamer-based methods are also discussed.
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Affiliation(s)
- Hongjie Xiong
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Jianhua Yan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Dongming Peng
- Department of Medicinal Chemistry, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, Hunan Province, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China.
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31
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Liu M, Yang T, Chen Z, Wang Z, He N. Differentiating breast cancer molecular subtypes using a DNA aptamer selected against MCF-7 cells. Biomater Sci 2019; 6:3152-3159. [PMID: 30349922 DOI: 10.1039/c8bm00787j] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides selected by systematic evolution of ligands by exponential enrichment (SELEX), which show great potential in the diagnosis and personalized therapy of cancers, due to their specific advantages over antibodies. In the past years, though great progress has been made in molecular subtyping of breast cancer, it remains a challenge in clinical medicine, which plays a crucial role in the treatment. In this study, a ssDNA aptamer MF3 against MCF-7 breast cancer cells was developed by Cell-SELEX for differentiating breast cancer molecular subtypes, which showed favorable specificity and binding affinity towards MCF-7 cells with a Kd value of 82.25 ± 25.14 nM. The aptamer could not only successfully distinguish MCF-7 breast cancer cells from MDA-MB-231 and SK-BR-3 breast cancer cells and MCF-10A human normal mammary epithelial cells, but also could differentiate MCF-7 cells from other cancer cells or normal cells. Moreover, both in vivo and in vitro fluorescence imaging studies demonstrated that aptamer MF3 was able to distinguish tumor-bearing mice and xenograft tissue sections of MCF-7 breast cancer cells from that of MDA-MB-231 and SK-BR-3 breast cancer cells. All these results suggested that aptamer MF3 is a potential tool for differentiating molecular subtypes and diagnosis of breast cancer.
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Affiliation(s)
- Mei Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China.
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32
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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33
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Yan X, Zhang H, Wang Z, Peng H, Tao J, Li XF, Chris Le X. Quantitative synthesis of protein-DNA conjugates with 1 : 1 stoichiometry. Chem Commun (Camb) 2018; 54:7491-7494. [PMID: 29917030 DOI: 10.1039/c8cc03268h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We describe here a binding-facilitated reaction strategy, enabling quantitative conjugation of DNA to native proteins with a desirable 1 : 1 stoichiometry. The technique takes advantage of the iterative affinity interaction and covalent binding processes to achieve complete conjugation. The complete conjugation obviates the need for separation of the protein-DNA conjugates as required by other DNA-protein conjugation methods.
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Affiliation(s)
- Xiaowen Yan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
| | - Zhixin Wang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G2G3, Canada.
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34
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Bioapplications of Cell-SELEX-Generated Aptamers in Cancer Diagnostics, Therapeutics, Theranostics and Biomarker Discovery: A Comprehensive Review. Cancers (Basel) 2018; 10:cancers10020047. [PMID: 29425173 PMCID: PMC5836079 DOI: 10.3390/cancers10020047] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Currently, functional single-stranded oligonucleotide probes, termed aptamers, generated by an iterative technology, Systematic Evolution of Ligands by Exponential Enrichment (SELEX), are utilized to selectively target molecules or cells with high affinity. Aptamers hold considerable promise as multifunctional molecules or conjugates for challenging nanotechnologies or bioapplications now and in the future. In this review, we first describe recent endeavors to select aptamers towards live cancer cells via cell-SELEX. We then introduce several characteristic applications of selected aptamers, especially in imaging, drug delivery and therapy. In part, these advances have been made possible via synthesis of aptamer-based nanomaterials, which, by their sizes, shapes, and physicochemical properties, allow such aptamer-nanomaterial complexes to function as signal reporters or drug carriers. We also describe how these aptamer-based molecular tools contribute to cancer biomarker discovery through high-affinity recognition of membrane protein receptors.
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35
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Shen C, Zeng K, Luo J, Li X, Yang M, Rasooly A. Self-Assembled DNA Generated Electric Current Biosensor for HER2 Analysis. Anal Chem 2017; 89:10264-10269. [PMID: 28859480 DOI: 10.1021/acs.analchem.7b01747] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have developed a new DNA self-assembly amplification technology that generates electric current for electrochemical biosensing. The new technology was used for detection of human epidermal growth factor receptor 2 (HER2). In our technology, an aptamer was utilized both as a ligand for recognition and as a signal generating reporter. The aptasensor is based on a sandwich format and a DNA primer on a HER2 aptamer initiates auxiliary DNA self-assembled on the electrode to form a long one-dimensional DNA. The resulting DNA is then reacted with molybdate to generate electrochemical current. The sensitivity of the aptasensor with DNA self-assembly was greater than that of the aptasensor without DNA self-assembly due to the extended length of the DNA strand. Aptasensor analysis of HER2 in serum of breast cancer patients and healthy individuals is highly correlated (R2 = 0.9924) with ELISA measurements, with a p value of 1.37 × 10-7. The analysis of HER2 in serum (confirmed by ELISA) suggests that HER2 levels in breast cancer patients are much higher than healthy individuals. For HER2 positive patients, the levels are higher than those of HER2 negative patients. After surgery, there is a drop of HER2 levels in serum, suggesting potential clinical applications of the new self-assembled DNA electric current generating biosensor. Unlike proteins, DNA is easily amplifiable. The DNA signal amplification method presented here enables effective current generation, which can find wide range of biomedical applications for protein detection.
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Affiliation(s)
- Congcong Shen
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Ke Zeng
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Junjun Luo
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Xiaoqing Li
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Minghui Yang
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Avraham Rasooly
- National Cancer Institute, National Institutes of Health , Rockville, Maryland 20850, United States
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36
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Motaghi H, Mehrgardi MA, Bouvet P. Carbon Dots-AS1411 Aptamer Nanoconjugate for Ultrasensitive Spectrofluorometric Detection of Cancer Cells. Sci Rep 2017; 7:10513. [PMID: 28874822 PMCID: PMC5585388 DOI: 10.1038/s41598-017-11087-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022] Open
Abstract
In the present study, a sensitive and selective signal-on method for aptamer based spectrofluorometric detection of cancer cells is introduced. AS1411, a nucleolin aptamer, is wrapped around water-soluble carbon dots and used as a probe for the detection of several types of cancer cells. Nucleolin, is overexpressed on the surface of cancer cells. Mouse breast 4T1, human breast MCF7, and human cervical HeLa cancer cells were selected as target cells, while human foreskin fibroblast cells HFFF-PI6 served as control cells. For the sensitive and selective spectrofluorimetric detection of target cancer cells in the presence of control cells, the cells were incubated in carbon dots-aptamer solutions, the cell suspensions were subsequently centrifuged and the fluorescence intensities were measured as an analytical signal. The specific targeting of cancer cells by AS1411 aptamers causes the release of carbon dots and enhances the fluorescence intensity. A calibration curve with a dynamic range between 10–4500 4T1 cells and detectability of roughly 7 cells was obtained. In addition, no significant change in the signal was detected by modifying the amount of human foreskin fibroblast control cells. Our results demonstrate similar responses to human MCF7 breast and cervical HeLa cancer cells.
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Affiliation(s)
- Hasan Motaghi
- Department of chemistry, University of Isfahan, Isfahan, 81746-73441, Iran
| | | | - Philippe Bouvet
- Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France.,Université de Lyon, Ecole Normale Supérieure de 3 Lyon, Lyon, France
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37
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Cui C, Zhang H, Wang R, Cansiz S, Pan X, Wan S, Hou W, Li L, Chen M, Liu Y, Chen X, Liu Q, Tan W. Recognition-then-Reaction Enables Site-Selective Bioconjugation to Proteins on Live-Cell Surfaces. Angew Chem Int Ed Engl 2017; 56:11954-11957. [PMID: 28840953 DOI: 10.1002/anie.201706285] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Indexed: 01/18/2023]
Abstract
Site-selective protein modification is a key step in facilitating protein functionalization and manipulation. To accomplish this, genetically engineered proteins were previously required, but the procedure was laborious, complex, and technically challenging. Herein we report the development of aptamer-based recognition-then-reaction to guide site-selective protein/DNA conjugation in a single step with outstanding selectivity and efficiency. As models, several proteins, including human thrombin, PDGF-BB, Avidin, and His-tagged recombinant protein, were studied, and the results showed excellent selectivity under mild reaction conditions. Taking advantage of aptamers as recognition elements with extraordinary selectivity and affinity, this simple preparation method can tag a protein in a complex milieu. Thus, with the aptamer obtained from cell-SELEX, real-time modification of live-cell membrane proteins can be achieved in one step without any pre-treatment.
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Affiliation(s)
- Cheng Cui
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Hui Zhang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Ruowen Wang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Life Sciences and College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Sena Cansiz
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Xiaoshu Pan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Weijia Hou
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Long Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China
| | - Yuan Liu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Life Sciences and College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xigao Chen
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Life Sciences and College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Weihong Tan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Life Sciences and College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
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38
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Cui C, Zhang H, Wang R, Cansiz S, Pan X, Wan S, Hou W, Li L, Chen M, Liu Y, Chen X, Liu Q, Tan W. Recognition-then-Reaction Enables Site-Selective Bioconjugation to Proteins on Live-Cell Surfaces. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706285] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Cheng Cui
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Hui Zhang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Jiangsu Key Laboratory of New Power Batteries; Jiangsu Collaborative Innovation Center of Biomedical Functional Materials; College of Chemistry and Materials Science; Nanjing Normal University; Nanjing 210023 China
| | - Ruowen Wang
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory; State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Life Sciences and College of Chemistry and Chemical Engineering; Aptamer Engineering Center of Hunan Province; Hunan University; Changsha Hunan 410082 China
| | - Sena Cansiz
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Xiaoshu Pan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Shuo Wan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Weijia Hou
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Long Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macau 999078 China
| | - Yuan Liu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory; State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Life Sciences and College of Chemistry and Chemical Engineering; Aptamer Engineering Center of Hunan Province; Hunan University; Changsha Hunan 410082 China
| | - Xigao Chen
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory; State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Life Sciences and College of Chemistry and Chemical Engineering; Aptamer Engineering Center of Hunan Province; Hunan University; Changsha Hunan 410082 China
| | - Weihong Tan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics; Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory; State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Life Sciences and College of Chemistry and Chemical Engineering; Aptamer Engineering Center of Hunan Province; Hunan University; Changsha Hunan 410082 China
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39
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Liu Z, Chen W, Han Y, Ouyang J, Chen M, Hu S, Deng L, Liu YN. A label-free sensitive method for membrane protein detection based on aptamer and AgNCs transfer. Talanta 2017; 175:470-476. [PMID: 28842019 DOI: 10.1016/j.talanta.2017.07.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/14/2017] [Accepted: 07/23/2017] [Indexed: 11/30/2022]
Abstract
Recently, membrane proteins have been considered as candidate cancer biomarkers and drug targets, due to their important roles in numerous physiological processes. Therefore, a facile, sensitive and quantitative detection of the membrane proteins is crucial for better understanding their roles in cancer cells and further validating their function in clinical research. We report a highly facile and sensitive detection method for membrane proteins on living cells in situ based on membrane protein-triggered release of cytosine (C)-rich single-stranded DNA (ssDNA) sequences, and the subsequent silver nanoclusters (AgNCs) transfer from polymer to C-rich ssDNA. The high-quantum yield and stable DNA-AgNCs allow the accurate detection of membrane proteins with facile operations and a common fluorescence spectrophotometer. The detection of protein tyrosine kinase-7 (PTK7), a membrane protein model, displays a response range from 30pM to 2nM with a detection limit of 12pM. The expression of PTK7 on single Hela cell and CCRF-CEM cell was calculated to be 7.5 × 10-19mol and 1.8 × 10-18mol, respectively. Given the simple and facile operation of this method, this detection platform can be applied as a universal strategy for ultrasensitive detection of membrane protein on cell in situ.
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Affiliation(s)
- Zhenjun Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Wansong Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Yajin Han
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Jiang Ouyang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Min Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Shengqiang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Liu Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China.
| | - You-Nian Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China.
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40
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Abstract
Conjugation of DNA to proteins is increasingly used in academia and industry to provide proteins with tags for identification or handles for hybridization to other DNA strands. Assay technologies such as immuno-PCR and proximity ligation and the imaging technology DNA-PAINT require DNA-protein conjugates. In DNA nanotechnology, the DNA handle is exploited to precisely position proteins by self-assembly. For these applications, site-selective conjugation is almost always desired because fully functional proteins are required to maintain the specificity of antibodies and the activity of enzymes. The introduction of a bioorthogonal handle at a specific position of a protein by recombinant techniques provides an excellent approach to site-specific conjugation, but for many laboratories and for applications where several proteins are to be labeled, the expression of recombinant proteins may be cumbersome. In recent years, a number of chemical methods that target conjugation to specific sites at native proteins have become available, and an overview of these methods is provided in this Account. Our laboratory has investigated DNA-templated protein conjugation (DTPC), which offers an alternative approach to site-selective conjugation of DNA to proteins. The method is inspired by the concept of DNA-templated synthesis where functional groups conjugated to DNA strands are preorganized by DNA hybridization to dramatically increase the reaction rate. In DPTC, we target metal binding sites in proteins to template selective covalent conjugation reactions. By chelation of a DNA-metal complex with a metal binding site of the protein, an electrophile on a second DNA strand is aligned for reaction with a lysine side chain on the protein in the proximity of the metal binding site. The method is quite general because approximately one-third of all wild-type proteins contain metal-binding sites, including many IgG antibodies, and it is also applicable to His-tagged proteins. This emerging field provides direct access to site-selective conjugates of DNA to commercially available proteins. In this Account, we introduce these methods to the reader and describe current developments and future aspects.
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Affiliation(s)
- Julie B. Trads
- Center for DNA Nanotechnology
at the Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Thomas Tørring
- Center for DNA Nanotechnology
at the Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology
at the Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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41
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Si Z, Xie B, Chen Z, Tang C, Li T, Yang M. Electrochemical aptasensor for the cancer biomarker CEA based on aptamer induced current due to formation of molybdophosphate. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2338-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Bi W, Bai X, Gao F, Lu C, Wang Y, Zhai G, Tian S, Fan E, Zhang Y, Zhang K. DNA-Templated Aptamer Probe for Identification of Target Proteins. Anal Chem 2017; 89:4071-4076. [PMID: 28267323 DOI: 10.1021/acs.analchem.6b04895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using aptamers as molecular probes for biomarker discovery has attracted a great deal of attention in recent years. However, it is still a big challenge to accurately identify those protein markers that are targeted by aptamers under physiological conditions due to weak and noncovalent aptamer-protein interactions. Herein, we developed an aptamer based dual-probe using DNA-templated chemistry and photo-cross-linking technique for the identification of target proteins that are recognized by aptamers. In this system, the aptamer was modified by a single strand DNA as binding probe (BP), and another complementary DNA with a photoactive group and reporter group was modified as capture probe (CP). BP was first added to recruit the binding protein via aptamer recognition, and subsequently CP was added to let the cross-linker close to the target via DNA self-assembly, and then a covalent bond between CP and its binding protein was achieved via photo-cross-linking reaction. The captured protein can be detected or affinity enrichment using the tag, finally identified by MS. By use of lysozyme as a model substrate, we demonstrated that this multiple functionalized probe can be utilized for a successful labeling and enrichment of target protein even under a complicated and real environment. Thus, a novel method to precisely identify the aptamer-targeted proteins has been developed and it has a potential application for discovery of aptamer-based biomarkers.
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Affiliation(s)
- Wenjing Bi
- Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China
| | - Xue Bai
- Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China
| | - Fan Gao
- Department of Chemistry, Nankai University , Tianjin 300071, China
| | - Congcong Lu
- Department of Chemistry, Nankai University , Tianjin 300071, China
| | - Ye Wang
- Department of Chemistry, Nankai University , Tianjin 300071, China
| | - Guijin Zhai
- Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China
| | - Shanshan Tian
- Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China
| | - Enguo Fan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg , 79104 Freiburg, Germany.,Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College , Beijing 100005, China
| | - Yukui Zhang
- Department of Chemistry, Nankai University , Tianjin 300071, China.,Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Kai Zhang
- Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China
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Zhang L, Wan S, Jiang Y, Wang Y, Fu T, Liu Q, Cao Z, Qiu L, Tan W. Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology. J Am Chem Soc 2017; 139:2532-2540. [PMID: 28121431 PMCID: PMC5519284 DOI: 10.1021/jacs.6b10646] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.
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Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Shuo Wan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Ying Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Yanyue Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Zhijuan Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
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44
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Hu L, Hu S, Guo L, Shen C, Yang M, Rasooly A. DNA Generated Electric Current Biosensor. Anal Chem 2017; 89:2547-2552. [PMID: 28219246 DOI: 10.1021/acs.analchem.6b04756] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In addition to its primary function as a genetic material, deoxyribonucleic acid (DNA) is also a potential biologic energy source for molecular electronics. For the first time, we demonstrate that DNA can generate a redox electric current. As an example of this new functionality, DNA generated redox current was used for electrochemical detection of human epidermal growth factor receptor 2 (HER2), a clinically important breast cancer biomarker. To induce redox current, the phosphate of the single stranded DNA aptamer backbone was reacted with molybdate to form redox molybdophosphate precipitate and generate an electrochemical current of ∼16.8 μA/μM cm2. This detection of HER2 was performed using a sandwich detection assay. A HER2 specific peptide was immobilized onto a gold electrode surface for capturing HER2 in buffer and serum. The HER2 specific aptamer was used as both ligand to bind the captured HER2 and to generate a redox current signal. When tested for HER2 detection, the electrochemical current generated by the aptasensor was proportional to HER2 concentration in the range of 0.01 to 5 ng/mL, with a current generated in the range of ∼6.37 to 31.8 μA/cm2 in both buffer and serum. This detection level is within the clinically relevant range of HER2 concentrations. This method of electrochemical signal amplification greatly simplifies the signal transduction of aptasensors, broadening their use for HER2 analysis. This novel approach of using the same aptamer as biosensor ligand and as transducer can be universally extended to other aptasensors for a wide array of biodetection applications. Moreover, electric currents generated by DNA or other nucleic acids can be used in molecular electronics or implanted devices for both power generation and measurement of output.
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Affiliation(s)
- Lanshuang Hu
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Shengqiang Hu
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Linyan Guo
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Congcong Shen
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Minghui Yang
- College of Chemistry and Chemical Engineering, Central South University , Changsha, China , 410083
| | - Avraham Rasooly
- National Cancer Institute, National Institutes of Health , Rockville, Maryland 20850, United States
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