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Cossu J, Ravelet C, Martel-Frachet V, Peyrin E, Boturyn D. Peptide-based CE-SELEX enables convenient isolation of aptamers specifically recognizing CD20-expressing cells. Bioorg Med Chem 2024; 110:117831. [PMID: 39004051 DOI: 10.1016/j.bmc.2024.117831] [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: 05/27/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024]
Abstract
The CD20 antigen is a key target for several diseases including lymphoma and autoimmune diseases. For over 20 years, several monoclonal antibodies were developed to treat CD20-related disorders. As many therapeutic proteins, their clinical use is however limited due to their nature with a costly biotechnological procedure and side effects such as the production of anti-drug neutralizing antibodies. Nucleic acid aptamers have some advantages over mAbs and are currently investigated for clinical use. We herein report the selection of DNA aptamer by using a peptide-based CE-SELEX (Capillary Electrophoresis-Systematic Evolution of Ligands by Exponential Enrichment) method. It was demonstrated that these aptamers bind specifically a CD20-expressing human cell line, with Kd estimated from isothermal titration calorimetry experiments in the micromolar range. This study demonstrates that the CE-SELEX is suitable as alternative method to the conventional Cell-SELEX to discover new cell-targeting compounds.
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Affiliation(s)
- Jordan Cossu
- University Grenoble Alpes, CNRS, DCM UMR 5250, 38058 Grenoble Cedex 9, France; University Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble Cedex 9, France
| | - Corinne Ravelet
- University Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble Cedex 9, France
| | - Véronique Martel-Frachet
- University Grenoble Alpes, IAB CNRS UMR5309, INSERM U1209, Allée des Alpes 38700, La Tronche, France; University PSL Research, EPHE, 5014 Paris, France
| | - Eric Peyrin
- University Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble Cedex 9, France.
| | - Didier Boturyn
- University Grenoble Alpes, CNRS, DCM UMR 5250, 38058 Grenoble Cedex 9, France.
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2
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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3
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Davodabadi F, Mirinejad S, Fathi-Karkan S, Majidpour M, Ajalli N, Sheervalilou R, Sargazi S, Rozmus D, Rahdar A, Diez-Pascual AM. Aptamer-functionalized quantum dots as theranostic nanotools against cancer and bacterial infections: A comprehensive overview of recent trends. Biotechnol Prog 2023; 39:e3366. [PMID: 37222166 DOI: 10.1002/btpr.3366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
Aptamers (Apts) are synthetic nucleic acid ligands that can be engineered to target various molecules, including amino acids, proteins, and pharmaceuticals. Through a series of adsorption, recovery, and amplification steps, Apts are extracted from combinatorial libraries of synthesized nucleic acids. Using aptasensors in bioanalysis and biomedicine can be improved by combining them with nanomaterials. Moreover, Apt-associated nanomaterials, including liposomes, polymeric, dendrimers, carbon nanomaterials, silica, nanorods, magnetic NPs, and quantum dots (QDs), have been widely used as promising nanotools in biomedicine. Following surface modifications and conjugation with appropriate functional groups, these nanomaterials can be successfully used in aptasensing. Advanced biological assays can use Apts immobilized on QD surfaces through physical interaction and chemical bonding. Accordingly, modern QD aptasensing platforms rely on interactions between QDs, Apts, and targets to detect them. QD-Apt conjugates can be used to directly detect prostate, ovarian, colorectal, and lung cancers or simultaneously detect biomarkers associated with these malignancies. Tenascin-C, mucin 1, prostate-specific antigen, prostate-specific membrane antigen, nucleolin, growth factors, and exosomes are among the cancer biomarkers that can be sensitively detected using such bioconjugates. Furthermore, Apt-conjugated QDs have shown great potential for controlling bacterial infections such as Bacillus thuringiensis, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Campylobacter jejuni, Staphylococcus aureus, and Salmonella typhimurium. This comprehensive review discusses recent advancements in the design of QD-Apt bioconjugates and their applications in cancer and bacterial theranostics.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sonia Fathi-Karkan
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mahdi Majidpour
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Narges Ajalli
- Department of Chemical Engineering, Faculty of Engineering, University of Tehran, Tehran, Iran
| | | | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Dominika Rozmus
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, Iran
| | - Ana M Diez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Quimica Analitica, Quimica Fisica e Ingenieria Quimica, Madrid, Spain
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4
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Teng X, Wang Y, You L, Wei L, Zhang C, Du Y. Screening a DNA Aptamer Specifically Targeting Integrin β3 and Partially Inhibiting Tumor Cell Migration. Anal Chem 2023; 95:12406-12418. [PMID: 37555842 PMCID: PMC10448441 DOI: 10.1021/acs.analchem.3c01995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
Due to its key roles in malignant tumor progression and reprograming of the tumor microenvironment, integrin β3 has attracted great attention as a new target for tumor therapy. However, the structure-function relationship of integrins β3 remains incompletely understood, leading to the shortage of specific and effective targeting probes. This work uses a purified extracellular domain of integrin β3 and integrin β3-positive cells to screen aptamers, specifically targeting integrin β3 in the native conformation on live cells through the SELEX approach. Following meticulous truncation and characterization of the initial aptamer candidates, the optimized aptamer S10yh2 was produced, exhibiting a low equilibrium dissociation constant (Kd) in the nanomolar range. S10yh2 displays specific recognition of cancer cells with varying levels of integrin β3 expression and demonstrates favorable stability in serum. Subsequent analysis of docking sites revealed that S10yh2 binds to the seven amino acid residues located in the core region of integrin β3. The S10yh2 aptamer can downregulate the level of integrin heterodimer αvβ3 on integrin β3 overexpressed cancer cells and partially inhibit cell migration behavior. In summary, S10yh2 is a promising probe with a small size, simple synthesis, good stability, high binding affinity, and selectivity. It therefore holds great potential for investigating the structure-function relationship of integrins.
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Affiliation(s)
- Xiaoyan Teng
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Yu Wang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liuxia You
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Lirong Wei
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Chao Zhang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuzhen Du
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
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5
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Xiong H, Li P, Cun F, Chen H, Kong J. Methylene-Blue-Encapsulated Metal-Organic-Framework-Based Electrochemical POCT Platform for Multiple Detection of Heavy Metal Ions in Milk. BIOSENSORS 2023; 13:783. [PMID: 37622869 PMCID: PMC10452309 DOI: 10.3390/bios13080783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
Considering the high risk of heavy metal ions (HMIs) transferring through the food chain and accumulating in milk, a flexible and facile point-of-care testing (POCT) platform is urgently needed for the accurate, sensitive, and highly selective on-site quantification of multiple HMIs in milk. In this work, a cost-effective disk with six screen-printed electrodes (SPEs) was designed for hand-held electrochemical detection. Metal organic frameworks (MOFs) were adopted to amplify and enhance the electrochemical signals of methylene blue (MB). Using differential pulse voltammetry (DPV) methods, low limits of detection for four HMIs (Cd2+, 0.039 ppb; Hg2+, 0.039 ppb; Pb2+, 0.073 ppb; and As3+, 0.022 ppb) were achieved within four minutes. Moreover, the quantitative POCT system was applied to milk samples. The advantages of low cost, ease of on-site implementation, fast response, and accuracy allow for the POCT platform to be used in practical monitoring applications for the quantitation of multiple HMIs in milk samples.
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Affiliation(s)
| | | | | | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai 200438, China
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6
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Wu L, Zhang Y, Wang Z, Zhang Y, Zou J, Qiu L. Aptamer-Based Cancer Cell Analysis and Treatment. Chemistry 2022; 11:e202200141. [PMID: 36264016 PMCID: PMC9583543 DOI: 10.1002/open.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Aptamers are a class of single-stranded DNA or RNA oligonucleotides that can exclusively bind to various targets with high affinity and selectivity. Regarded as "chemical antibodies", aptamers possess several intrinsic advantages, including easy synthesis, convenient modification, high programmability, and good biocompatibility. In recent decades, many studies have demonstrated the superiority of aptamers as molecular tools for various biological applications, particularly in the area of cancer theranostics. In this review, we focus on recent progress in developing aptamer-based strategies for the precise analysis and treatment of cancer cells.
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Affiliation(s)
- Limei Wu
- 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 ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Yutong Zhang
- 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 ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Zhimin Wang
- 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 ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Yue Zhang
- 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 ProvinceHunan UniversityChangsha, Hunan410082P. R. China
| | - Jianmei Zou
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, College of Chemistry and BioengineeringGuilin University of TechnologyGuilin, Guangxi541004P. R. China
| | - Liping Qiu
- 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 ProvinceHunan UniversityChangsha, Hunan410082P. R. China
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7
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Yoshida K, Hayashi T, Takinoue M, Onoe H. Repeatable detection of Ag + ions using a DNA aptamer-linked hydrogel biochemical sensor integrated with microfluidic heating system. Sci Rep 2022; 12:9692. [PMID: 35690676 PMCID: PMC9188593 DOI: 10.1038/s41598-022-13970-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/31/2022] [Indexed: 01/23/2023] Open
Abstract
This paper describes repeatable detection of Ag+ ions using a DNA aptamer-linked hydrogel biochemical sensor integrated with a microfluidic heating system. Biochemical sensors that respond to chemical compounds and produce detectable signals have a critical role in many aspects of modern society. In particular, the repeatable measurement of environmental information such as toxic substances including Ag+ ions could be expected to improve the environment. The DNA aptamer is an attractive candidate because of the stability and the selectivity of binding to chemicals. However, previous DNA aptamer biochemical sensors could not measure repeatedly because those sensors did not have initializing functions. To overcome this challenge, we proposed a DNA aptamer-linked hydrogel biochemical sensor integrated with the microfluidic heating system enabling repeatable detection of Ag+ ions. The binding Ag+ ions are dissociated by heating and flushing through the integrated microfluidic heating device. The DNA aptamer-linked hydrogel had the capability to detect a wide range of Ag+ ion concentrations (10-5-10 mM) including a toxic range for various aquatic organisms. Finally, we demonstrated the repeatable detection of the Ag+ ions. These results indicated that our proposed biochemical sensor is expected to use for long-term monitoring with high stability in ambient temperature and low power consumption.
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Affiliation(s)
- Koki Yoshida
- Graduate School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, 223-8522, Japan
| | - Tomoki Hayashi
- Graduate School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, 223-8522, Japan
| | - Masahiro Takinoue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-Ku, Yokohama, 226-8502, Japan
| | - Hiroaki Onoe
- Graduate School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, 223-8522, Japan. .,Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-Ku, Yokohama, 223-8522, Japan.
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8
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Advances in aptamer-based nuclear imaging. Eur J Nucl Med Mol Imaging 2022; 49:2544-2559. [PMID: 35394153 DOI: 10.1007/s00259-022-05782-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/26/2022] [Indexed: 01/12/2023]
Abstract
Aptamers are short oligonucleotides that bind to specific target molecules. They have been extensively explored in biomedical applications, including biosensing, medical imaging, and disease treatment. Their adjustable affinity for specific biomarkers stimulates more translational efforts, such as nuclear imaging of tumors in preclinical and clinical settings. In this review, we present recent advances of aptamer-based nuclear imaging and compare aptamer tracers with other biogenic probes in forms of peptides, nanobodies, monoclonal antibodies, and antibody fragments. Fundamental properties of aptamer-based radiotracers are highlighted and potential directions to improve aptamer's imaging performance are discussed. Despite many translational obstacles to overcome, we envision aptamers to be a versatile tool for cancer nuclear imaging in the near future.
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Xu J, Xiang J, Chen J, Wan T, Deng H, Li D. High sensitivity detection of tumor cells in biological samples using a multivalent aptamer strand displacement strategy. Analyst 2022; 147:634-644. [PMID: 35040831 DOI: 10.1039/d1an01949j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Monitoring the cell surface-expressed nucleolin facilitates early cancer diagnosis. Herein, we developed a multivalent aptamer displacement strand duplex strategy on cell membranes using a multi-receptor co-recognition design for improving the sensitivity and specificity of cancer cell recognition with an ultra-low background. The AS1411 aptamer labeled with the FAM fluorophore can be quenched using a partial complementary sequence modified with a BHQ1 tag which is partially hybridized with the AS1411 aptamer to create a receptor-activating aptamer. The multi-AS1411 activable probe based on the strand displacement strategy was constructed using multiple copies of the structure-switching AS1411 aptamer (bearing a short poly-A tail) linked together using the poly-T long chain (as a scaffold) which was synthesized by Terminal Deoxynucleotidyl Transferase (TDT)-mediated extension. We demonstrated the promising efficacy and sensitivity of our method in recognizing tumor cells in both cell mixtures and clinical cytology specimens. Due to its simple and fast operation with excellent cell recognition sensitivity and accuracy, it is expected to achieve the detection of low abundance target cells. Our approach will have broad application in clinical rapid detection and personalized medicine.
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Affiliation(s)
- Jieru Xu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jiahui Xiang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Jialing Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Tao Wan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongli Deng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Dairong Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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10
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Ali GK, Omer KM. Molecular imprinted polymer combined with aptamer (MIP-aptamer) as a hybrid dual recognition element for bio(chemical) sensing applications. Review. Talanta 2022; 236:122878. [PMID: 34635258 DOI: 10.1016/j.talanta.2021.122878] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
The development of diagnostic devices based on memetic molecular recognitions are becoming highly promising due to high specificity, sensitivity, stability, and low-cost comparing to natural molecular recognition. During the last decade, molecular imprinted polymers (MIPs) and aptamer have shown dramatic enhancement in the molecular recognition characteristics for bio(chemical) sensing applications. Recently, MIP-aptamer, as an emerging hybrid recognition element, merged the advantages of the both recognition components. This dual recognition-based sensor has shown improved properties and desirable features, such as high sensitivity, low limit of detection, high stability under harsh environmental conditions, high binding affinity, and superior selectivity. Hybrid MIP-aptamer as dual recognition element, was used in the real sample analysis, such as detection of proteins, neurotransmitters, environmental pollutants, biogenic compounds, small ions, explosives, virus detections and pharmaceuticals. This review focuses on a comprehensive overview of the preparation strategies of various MIP-aptamer recognition elements, mechanism of formation of MIP-aptamer, and detection of various target molecules in different matrices.
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Affiliation(s)
- Gona K Ali
- Center for Biomedical Analysis, Department of Chemistry, College of Science, University of Sulaimani, Qliasan St, 46002, Slemani City, Kurdistan Region, Iraq
| | - Khalid M Omer
- Center for Biomedical Analysis, Department of Chemistry, College of Science, University of Sulaimani, Qliasan St, 46002, Slemani City, Kurdistan Region, Iraq.
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Lighting up ATP in cells and tissues using a simple aptamer-based fluorescent probe. Mikrochim Acta 2021; 188:352. [PMID: 34554325 PMCID: PMC8459148 DOI: 10.1007/s00604-021-05012-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/28/2021] [Indexed: 01/02/2023]
Abstract
Extracellular ATP as a purinergic signaling molecule, together with ATP receptor, are playing an important role in tumor growth, therapy resistance, and host immunity suppression. Meanwhile ATP is a crucial indicator for cellular energy status and viability, thus a vital variable for tissue regeneration and in vitro tissue engineering. Most recent studies on COVID-19 virus suggest infection caused ATP deficit and release as a major characterization at the early stage of the disease and major causes for disease complications. Thus, imaging ATP molecule in both cellular and extracellular contexts has many applications in biology, engineering, and clinics. A sensitive and selective fluorescence “signal-on” probe for ATP detection was constructed, based on the base recognition between a black hole quencher (BHQ)-labeled aptamer oligonucleotide and a fluorophore (Cy5)-labeled reporter flare. The probe was able to detect ATP in solution with single digit µM detection limit. With the assistance of lipofectamine, this probe efficiently entered and shined in the model cells U2OS within 3 h. Further application of the probe in specific scenery, cardio-tissue engineering, was also tested where the ATP aptamer complex was able to sense cellular ATP status in a semi-quantitative manner, representing a novel approach for selection of functional cardiomyocytes for tissue engineering. At last a slight change in probe configuration in which a flexible intermolecular A14 linker was introduced granted regeneration capability. These data support the application of this probe in multiple circumstances where ATP measurement or imaging is on demand.
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12
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Verdian A, Rouhbakhsh Z, Fooladi E. An ultrasensitive platform for PCB77 detection: New strategy for liquid crystal-based aptasensor fabrication. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123531. [PMID: 32721640 DOI: 10.1016/j.jhazmat.2020.123531] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 05/29/2023]
Abstract
Polychlorinated biphenyls (PCBs) are considered persistent bio-accumulative toxicants which threats global food safety and environmental health. Traditional analytical techniques for detection of PCBs are time-consuming and they do not satisfy urgent need for rapid and accurate monitoring of these persistent pollutants. Biosensor technology may be promising in this respect. Here we demonstrate a novel liquid crystal (LC)-based aptasensing platform as a promising label-free and rapid biosensor for PCB77 detection. This novel molecular strategy utilize triple-helix molecular conformational switch which is mediated formation of duplex on sensing platform in presence of target. Duplex forming leads to optical change from dark to bright in a liquid crystal based aptasensor. The limit of quantification of the LC-aptasensor to PCB77 is 1.5 × 10-5 μg/L with comparable selectivity. Besides, we also demonstrated that this system is able to detect PCB77 in tap water, environmental water and milk. This strategy has potential for label-free and portable detection of different targets without any aptamer sequence length restrictions.
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Affiliation(s)
- Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran.
| | - Zeinab Rouhbakhsh
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
| | - Ebrahim Fooladi
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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13
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, 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, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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14
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Yi J, Xiao W, Li G, Wu P, He Y, Chen C, He Y, Ding P, Kai T. The research of aptamer biosensor technologies for detection of microorganism. Appl Microbiol Biotechnol 2020; 104:9877-9890. [PMID: 33047168 DOI: 10.1007/s00253-020-10940-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/21/2022]
Abstract
The activities and transmissions of microorganisms are closely related to human, and all kinds of diseases caused by pathogenic microorganisms have attracted attention in the world and brought many challenges to human health and public health. The traditional microbial detection technologies have characteristics of longer detection cycle and complicated processes, therefore, which can no longer meet the detection requirements in the field of public health. At present, it is the focus to develop and design a novel, rapid, and simple microbial detection method in the field of public health. Herein, this article summarized the development of aptamer biosensor technologies for detection of microorganism in the aspect of bacteria, viruses, and toxins in detail, including optical aptamer sensors such as fluorometry and colorimetry, electrochemical aptamer sensors, and other technologies combined with aptamer. KEY POINTS: • Aptamer biosensor is a good platform for microbial detection. • Aptamer biosensors include optical sensors and electrochemical sensors. • Aptamer sensors have been widely used in the detection of bacteria, viruses, and other microorganisms.
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Affiliation(s)
- Jiecan Yi
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China.,School of Public Health, Changsha Medical University, Changsha, 410219, Hunan, China
| | - Wen Xiao
- Hunan Institute of Food Quality Supervision Inspection and Research, Changsha, 410000, Hunan, China
| | - Guiyin Li
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541014, Guangxi, China
| | - Pian Wu
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Yayuan He
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Cuimei Chen
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Yafei He
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Ping Ding
- Xiang Ya School of Public Health, Central South University, Changsha, 410078, Hunan, China.
| | - Tianhan Kai
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410078, Hunan, China.
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15
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Xiong M, Liu Q, Tang D, Liu L, Kong G, Fu X, Yang C, Lyu Y, Meng HM, Ke G, Zhang XB. “Apollo Program” in Nanoscale: Landing and Exploring Cell-Surface with DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2020; 3:2723-2742. [DOI: 10.1021/acsabm.9b01193] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Qin Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiaoyi Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Chan Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
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16
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Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based immunoassay and aptamer assay: A review. Electrophoresis 2020; 41:414-433. [PMID: 31975407 DOI: 10.1002/elps.201900426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/31/2022]
Abstract
Over the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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17
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Liu L, Dong C, Li X, Li S, Ma B, Zhao B, Li X, Liang Z, Yang K, Zhang L, Zhang Y. Antibody-Free Hydrogel with the Synergistic Effect of Cell Imprinting and Boronate Affinity: Toward the Selective Capture and Release of Undamaged Circulating Tumor Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904199. [PMID: 31971662 DOI: 10.1002/smll.201904199] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/15/2019] [Indexed: 06/10/2023]
Abstract
The selective and highly efficient capture of circulating tumor cells (CTCs) from blood and their subsequent release without damage are very important for the early diagnosis of tumors and for understanding the mechanism of metastasis. Herein, a universal strategy is proposed for the fabrication of an antibody-free hydrogel that has a synergistic effect by featuring microinterfaces obtained by cell imprinting and molecular recognition conferred by boronate affinity. With this artificial antibody, highly efficient capture of human hepatocarcinoma SMMC-7721 cells is achieved: as many as 90.3 ± 1.4% (n = 3) cells are captured when 1 × 105 SMMC-7721 cells are incubated on a 4.5 cm2 hydrogel, and 99% of these captured cells are subsequently released without any loss of proliferation ability. In the presence of 1000 times as many nontarget cells, namely, leukaemia Jurkat cells, the SMMC-7721 cells can be captured with an enrichment factor as high as 13.5 ± 3.2 (n = 3), demonstrating the superior selectivity of the artificial antibody for the capture of the targeted CTCs. Most importantly, the SMMC-7721 cells can be successfully captured even when spiked into whole blood, indicating the great promise of this approach for the further molecular characterization of CTCs.
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Affiliation(s)
- Lukuan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Chengyong Dong
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Xinwei Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Food Science and Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Senwu Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Baofu Ma
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiao Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Davydova A, Krasitskaya V, Vorobjev P, Timoshenko V, Tupikin A, Kabilov M, Frank L, Venyaminova A, Vorobyeva M. Reporter-recruiting bifunctional aptasensor for bioluminescent analytical assays. RSC Adv 2020; 10:32393-32399. [PMID: 35516485 PMCID: PMC9056652 DOI: 10.1039/d0ra05117a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/21/2020] [Indexed: 12/26/2022] Open
Abstract
A novel structure-switching bioluminescent 2′-F-RNA aptasensor consists of analyte-binding and obelin-recruiting modules, joined into a bi-specific aptamer construct.
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Affiliation(s)
- Anna Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Vasilisa Krasitskaya
- Institute of Biophysics SB RAS
- Federal Research Center “Krasnoyarsk Science Center SB RAS”
- Krasnoyarsk 660036
- Russia
| | - Pavel Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
- Novosibirsk State University
- 630090 Novosibirsk
| | - Valentina Timoshenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Ludmila Frank
- Institute of Biophysics SB RAS
- Federal Research Center “Krasnoyarsk Science Center SB RAS”
- Krasnoyarsk 660036
- Russia
- Siberian Federal University
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
| | - Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS
- Novosibirsk 630090
- Russia
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19
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Witt S, Scheper T, Walter J. Production of polycaprolactone nanoparticles with hydrodynamic diameters below 100 nm. Eng Life Sci 2019; 19:658-665. [PMID: 32624959 PMCID: PMC6999587 DOI: 10.1002/elsc.201800214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/27/2019] [Accepted: 07/31/2019] [Indexed: 12/24/2022] Open
Abstract
Cancer is a worldwide increasing burden and its therapy is often challenging and causes severe side effects in healthy tissue. If drugs are loaded into nanoparticles, side effects can be reduced, and efficiency can be increased via the enhanced permeability and retention effect. This effect is based on the fact that nanoparticles with sizes from 10 to 200 nm can accumulate in tumor tissue due to their leaky vasculature. In this work, we produced polycaprolactone (PCL) in the sizes 1.8, 5.4, and 13.6 kDa and were able to produce spherical shaped nanoparticles with mean diameters of 64 ± 19 nm out of the PCL5.4 and 45 ± 8 nm out of the PCL13.6 reproducibly. By encapsulation of paclitaxel the diameter of that nanoparticles did not increase, and we were able to encapsulate 73 ± 7 fmol paclitaxel per 1000 particles in the PCL5.4-nanoparticles and 35 ± 8 fmol PTX per 1000 PCL13.6-nanoparticles. Furthermore, we coupled the aptamer S15 to preformed PCL5.4-nanoparticles resulting in particles with a hydrodynamic diameter of 153 nm. This offers the opportunity to use these nanoparticles for targeted drug delivery.
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Affiliation(s)
- Sandra Witt
- Institut für Technische Chemie HannoverLeibniz Universität HannoverHannoverGermany
| | - Thomas Scheper
- Institut für Technische Chemie HannoverLeibniz Universität HannoverHannoverGermany
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20
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Verdian A, Fooladi E, Rouhbakhsh Z. Recent progress in the development of recognition bioelements for polychlorinated biphenyls detection: Antibodies and aptamers. Talanta 2019; 202:123-135. [PMID: 31171160 DOI: 10.1016/j.talanta.2019.04.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/06/2023]
Abstract
Polychlorinated biphenyls (PCBs) are persistent pollutants, which have expanded in foods and the environment. Detection of PCBs is considered essential due to recognized side-effects of PCBs on health and the public concerns in this regard. On the other hand, due to the trace levels of these organic chlorine compounds, reliable and sensitive assays must be developed. Recognition elements are essential parts of analytical detection assays and sensors of PCBs since these elements are involved in the selective identification of the analytes of interest. Understanding the fundamentals of the recognition elements of PCBs and the benefits of the sensor strategies result in the development of next-generation recognition devices. This review aimed to highlight the recent progress in the recognition elements as key parts of biosensors. We initially, focused on the developed antibody-based biosensors for the detection of PCBs, followed by discussing the aptamers as novel recognition elements. Furthermore, the recent advancement in the development of aptamer-based solid phase extractions has been evaluated. These findings could contribute to improving the design of commercial PCB-kits in the future.
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Affiliation(s)
- Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran.
| | - Ebrahim Fooladi
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
| | - Zeinab Rouhbakhsh
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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21
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Control of capillary behavior through target-responsive hydrogel permeability alteration for sensitive visual quantitative detection. Nat Commun 2019; 10:1036. [PMID: 30850603 PMCID: PMC6408548 DOI: 10.1038/s41467-019-08952-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022] Open
Abstract
DNA hydrogels have received considerable attention in analytical science, however, some limitations still exist in the applications of intelligent hydrogels. In this paper, we describe a way to prepare gel film in a capillary tube based on the thermal reversible principle of DNA hydrogel and the principle of capillary action. Because of the slight change in the internal structure of gel, its permeability can be increased by the addition of some specific targets. The capillary behavior is thus changed due to the different permeability of the hydrogel film. The duration time of the target solution flowing through the capillary tube with a specified length is used to quantify this change. With this proposed method, ultra-trace DNA hydrogel (0.01 μL) is sufficient to realize the sensitive detection of cocaine without the aid of other instruments, which has a low detection limit (1.17 nM) and good selectivity. DNA hydrogels have received considerable attention in analytical science but limitations still exist in the applications of intelligent hydrogels. Here, the authors describe a DNA hydrogel sensor for quantitative detection of cocaine based on the permeability change in a DNA hydrogel film.
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22
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Liu L, Yang K, Dai Z, Liang Z, Zhang L, Peng X, Zhang Y. Cell-imprinted polydimethylsiloxane for the selective cell adhesion. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Development and characterization of novel 2'-F-RNA aptamers specific to human total and glycated hemoglobins. Anal Biochem 2019; 570:43-50. [PMID: 30742800 DOI: 10.1016/j.ab.2019.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 02/07/2023]
Abstract
Aptamers are short DNA and RNA fragments which bind their molecular targets with affinity and specificity comparable to those of antibodies. Here, we describe the selection of novel 2'-F-RNA aptamers against total human hemoglobin or its glycated form HbA1c. After SELEX and high-throughput sequencing of the enriched libraries, affinities and specificities of candidate aptamers and their truncated variants were examined by the solid-phase bioluminescent assay. As a result, we identified aptamers specific to both hemoglobins or only glycated HbA1c. The developed 2'-F-RNA aptamers have shown their applicability for detection of total and glycated hemoglobin in one sample.
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24
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Liu Y, Zhu Z, Wang C, Gao R, Yang X, Liu S. Responsive surface bioaffinity binding to construct flexible and sensitive electrochemical aptasensors. Analyst 2019; 144:2130-2137. [DOI: 10.1039/c8an02313a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A responsive surface bioaffinity binding strategy was developed for the fabrication of simple, flexible and amplified electrochemical aptasensors.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Zhencai Zhu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Chao Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Rui Gao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xiaoyan Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Shufeng Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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Chen D, Sun D, Wang Z, Qin W, Chen L, Zhou L, Zhang Y. A DNA nanostructured aptasensor for the sensitive electrochemical detection of HepG2 cells based on multibranched hybridization chain reaction amplification strategy. Biosens Bioelectron 2018; 117:416-421. [PMID: 29966920 DOI: 10.1016/j.bios.2018.06.041] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/19/2022]
Abstract
Sensitive detection of cancer cells is beneficial to the early diagnosis of cancer and individual treatment. In the present study, a DNA nanostructured aptasensor was used for the sensitive electrochemical detection of human liver hepatocellular carcinoma cells (HepG2) based on multibranched hybridization chain reaction amplification strategy. We established a well-designed platform by immobilizing DNA tetrahedron, a three-dimensional DNA nanostructure, on the gold electrode to capture HepG2 cells more specifically and efficiently. Meanwhile, functional hybrid nanoprobes consisted of MIL-101@AuNPs (Au nanoparticles), numerous hemin/G-quadruplex DNAzyme from multibranched hybridization chain reaction, and natural horseradish peroxidase (HRP) was designed. The hybrid nanoprobes possessed the functions of specific discernment and enzymatic signal amplification simultaneously. With the help of nanoprobes, HepG2 cells were recognized and captured to form a DNA tetrahedron-cell-nanoprobe sandwich-like structure on the electrode surface. The lower detection limit of this established cytosensor is 5 cells per ml. Moreover, it delivered a broad detection range from 102 to 107 cells per ml. The results revealed that the as-proposed cytosensor may be utilized as a powerful tool for early diagnosis of cancer in the future.
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Affiliation(s)
- Dabin Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Duanping Sun
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Zhiru Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Weiwei Qin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China
| | - Ledu Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, China.
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26
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Li Y, Jiao X, Du X, Wang F, Wei Q, Wen Y, Zhang X. Wettability alteration in a functional capillary tube for visual quantitative point of care testing. Analyst 2018; 143:3001-3005. [PMID: 29888353 DOI: 10.1039/c8an00735g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Capillarity is an extremely common physical-chemical phenomenon related to wettability in nature, which has wide theoretical and practical interest. Herein, we reported a facile sensing device based on capillary force change in a vertical capillary tube. In this height-based capillary sensor (HCS), the inner surface of the capillary tube was modified with a layer of molecules with wetting responsibility based on the well-known simple surface chemistry. With targets in different concentrations, the wettability of the surface modified with responsive molecules would produce different changes. The responsive surfaces would change the capillary force of the vertical capillary tube, and result in different column heights. Like a thermometer, H+ and phenol have been quantified visually based on the height of the liquid inside the capillary tube.
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Affiliation(s)
- Yansheng Li
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Xiangyu Jiao
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Xin Du
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Fang Wang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Qianhui Wei
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Yongqiang Wen
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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27
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Yang H, Zhang Y, Zhang L, Cui K, Ge S, Huang J, Yu J. Stackable Lab-on-Paper Device with All-in-One Au Electrode for High-Efficiency Photoelectrochemical Cyto-Sensing. Anal Chem 2018; 90:7212-7220. [PMID: 29782145 DOI: 10.1021/acs.analchem.8b00153] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Highly conductive, robust, and multifunctional integrated paper-supported electrodes are requisite to fulfill the promise of paper-based analytical application. Herein, an all-in-one Au electrode comprising of detection zone, waterproof electronic bridge, and signal output contactor was engineered via combining the double-sided growth method with the secondary wax-printing. Benefiting from the strongly omnidirectional conductivity and desirably mechanical robustness of the as-prepared electrode, a stackable lab-on-paper cyto-device integrated with high-efficiency photoelectrochemical strategy was developed for the MCF-7 cells assay. Specifically, the detection zone of the electrode, serving as the signal generator, was functionalized with a low-toxic cosensitized structure composed of corn-like ZnO nanorods, graphene quantum dots (GQDs), and Ag2Se QDs. With the proximity control of DNA hairpin-based aptamer probe (DHAP), a strong photocurrent could be promoted by the activated cosensitization effect and collected on the signal output contactor via the electron transport of waterproof electronic bridge. Upon the MCF-7 cells recognition, the DHAP switched from closed to open state with the formation of DNA-cell bioconjugates and the spatial separation of Ag2Se QDs linked on the terminal of DHAP from the electrode surface. The photocurrent was noticeably decreased due to the double inhibition of steric hindrance effect and vanished cosensitization effect. Based on the target-triggered photocurrent attenuation, the sensitive detection of target cells was achieved. This work not only provided a unique method for paper-based electrode preparation but also offered a powerful platform for the highly sensitive photoelectrochemical bioanalysis.
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Affiliation(s)
- Hongmei Yang
- School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , China
| | - Yan Zhang
- School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , China
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials , University of Jinan , Jinan 250022 , China
| | - Kang Cui
- School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research , University of Jinan , Jinan 250022 , China
| | - Jiadong Huang
- School of Biological Science and Technology , University of Jinan , Jinan 250022 , China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , China
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Park KS. Nucleic acid aptamer-based methods for diagnosis of infections. Biosens Bioelectron 2018; 102:179-188. [PMID: 29136589 PMCID: PMC7125563 DOI: 10.1016/j.bios.2017.11.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.
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Affiliation(s)
- Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Wang Y, Zhu Y, Hu Y, Zeng G, Zhang Y, Zhang C, Feng C. How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703305. [PMID: 29450972 DOI: 10.1002/smll.201703305] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/23/2017] [Indexed: 06/08/2023]
Abstract
With high binding affinity, porous structures, safety, green, programmability, etc., DNA hydrogels have gained increasing recognition in the environmental field, i.e., advanced treatment technology of water and analysis of specific pollutants. DNA hydrogels have been demonstrated as versatile potential adsorbents, immobilization carriers of bioactive molecules, catalysts, sensors, etc. Moreover, altering components or choosing appropriate functional DNA optimizes environment-oriented hydrogels. However, the lack of comprehensive information hinders the continued optimization. The principle used to fabricate the most suitable hydrogels in terms of the requirements is the focus of this Review. First, different fabrication strategies are introduced and the ideal characteristic for environmental applications is in focus. Subsequently, recent environmental applications and the development of diverse DNA hydrogels regarding their synthesis mechanism are summarized. Finally, the Review provides an insight into the remaining challenging and future perspectives in environmental applications.
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Affiliation(s)
- Yingrong Wang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yuan Zhu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yi Hu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yi Zhang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Chongling Feng
- Research Center of Environmental Science and Engineering, Center South University of Forestry and Technology, Shaoshan South Road, Changsha, 410004, China
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Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A. Int J Mol Sci 2018; 19:ijms19020642. [PMID: 29495282 PMCID: PMC5855864 DOI: 10.3390/ijms19020642] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/09/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023] Open
Abstract
New, as yet undiscovered aptamers for Protein A were identified by applying next generation sequencing (NGS) to a previously selected aptamer pool. This pool was obtained in a classical SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiment using the FluMag-SELEX procedure followed by cloning and Sanger sequencing. PA#2/8 was identified as the only Protein A-binding aptamer from the Sanger sequence pool, and was shown to be able to bind intact cells of Staphylococcus aureus. In this study, we show the extension of the SELEX results by re-sequencing of the same aptamer pool using a medium throughput NGS approach and data analysis. Both data pools were compared. They confirm the selection of a highly complex and heterogeneous oligonucleotide pool and show consistently a high content of orphans as well as a similar relative frequency of certain sequence groups. But in contrast to the Sanger data pool, the NGS pool was clearly dominated by one sequence group containing the known Protein A-binding aptamer PA#2/8 as the most frequent sequence in this group. In addition, we found two new sequence groups in the NGS pool represented by PA-C10 and PA-C8, respectively, which also have high specificity for Protein A. Comparative affinity studies reveal differences between the aptamers and confirm that PA#2/8 remains the most potent sequence within the selected aptamer pool reaching affinities in the low nanomolar range of KD = 20 ± 1 nM.
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31
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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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32
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Yang B, Chen B, He M, Yin X, Xu C, Hu B. Aptamer-Based Dual-Functional Probe for Rapid and Specific Counting and Imaging of MCF-7 Cells. Anal Chem 2018; 90:2355-2361. [PMID: 29308635 DOI: 10.1021/acs.analchem.7b04927] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Development of multimodal detection technologies for accurate diagnosis of cancer at early stages is in great demand. In this work, we report a novel approach using an aptamer-based dual-functional probe for rapid, sensitive, and specific counting and visualization of MCF-7 cells by inductively coupled plasma-mass spectrometry (ICP-MS) and fluorescence imaging. The probe consists of a recognition unit of aptamer to catch cancer cells specifically, a fluorescent dye (FAM) moiety for fluorescence resonance energy transfer (FRET)-based "off-on" fluorescence imaging as well as gold nanoparticles (Au NPs) tag for both ICP-MS quantification and fluorescence quenching. Due to the signal amplification effect and low spectral interference of Au NPs in ICP-MS, an excellent linearity and sensitivity were achieved. Accordingly, a limit of detection of 81 MCF-7 cells and a relative standard deviation of 5.6% (800 cells, n = 7) were obtained. The dynamic linear range was 2 × 102 to 1.2 × 104 cells, and the recoveries in human whole blood were in the range of 98-110%. Overall, the established method provides quantitative and visualized information on MCF-7 cells with a simple and rapid process and paves the way for a promising strategy for biomedical research and clinical diagnostics.
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Affiliation(s)
- Bin Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, China
| | - Beibei Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, China
| | - Man He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, China
| | - Xiao Yin
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, China
| | - Chi Xu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, China
| | - Bin Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, China
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33
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Rydahl MG, Hansen AR, Kračun SK, Mravec J. Report on the Current Inventory of the Toolbox for Plant Cell Wall Analysis: Proteinaceous and Small Molecular Probes. FRONTIERS IN PLANT SCIENCE 2018; 9:581. [PMID: 29774041 PMCID: PMC5943554 DOI: 10.3389/fpls.2018.00581] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
Plant cell walls are highly complex structures composed of diverse classes of polysaccharides, proteoglycans, and polyphenolics, which have numerous roles throughout the life of a plant. Significant research efforts aim to understand the biology of this cellular organelle and to facilitate cell-wall-based industrial applications. To accomplish this, researchers need to be provided with a variety of sensitive and specific detection methods for separate cell wall components, and their various molecular characteristics in vitro as well as in situ. Cell wall component-directed molecular detection probes (in short: cell wall probes, CWPs) are an essential asset to the plant glycobiology toolbox. To date, a relatively large set of CWPs has been produced-mainly consisting of monoclonal antibodies, carbohydrate-binding modules, synthetic antibodies produced by phage display, and small molecular probes. In this review, we summarize the state-of-the-art knowledge about these CWPs; their classification and their advantages and disadvantages in different applications. In particular, we elaborate on the recent advances in non-conventional approaches to the generation of novel CWPs, and identify the remaining gaps in terms of target recognition. This report also highlights the addition of new "compartments" to the probing toolbox, which is filled with novel chemical biology tools, such as metabolic labeling reagents and oligosaccharide conjugates. In the end, we also forecast future developments in this dynamic field.
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Affiliation(s)
- Maja G. Rydahl
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Aleksander R. Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Stjepan K. Kračun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- GlycoSpot IVS, Frederiksberg, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- *Correspondence: Jozef Mravec
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34
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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35
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Zhang Z, Tao C, Yin J, Wang Y, Li Y. Enhancing the response rate of strand displacement-based electrochemical aptamer sensors using bivalent binding aptamer-cDNA probes. Biosens Bioelectron 2017; 103:39-44. [PMID: 29278811 DOI: 10.1016/j.bios.2017.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022]
Abstract
Electrochemical aptamer (EA) sensors based on aptamer-cDNA duplex probes (cDNA: complementary DNA) and target induced strand displacement (TISD) recognition are sensitive, selective and capable of detecting a wide variety of target analytes. While substantial research efforts have focused on engineering of new signaling mechanisms for the improvement of sensor sensitivity, little attention was paid to the enhancement of sensor response rate. Typically, the previous TISD based EA sensors exhibited relatively long response times larger than 30min, which mainly resulted from the suboptimal aptamer-cDNA probe structure in which most of aptamer bases were paired to the cDNA bases. In an effort to improve the response rate of this type of sensors, we report here the rational engineering of a quickly responsive and sensitive aptamer-cDNA probe by employing the conception of bivalent interaction in supramolecular chemistry. We design a bivalent cDNA strand through linking two short monovalent cDNA sequences, and it is simultaneously hybridized to two electrode-immobilized aptamer probes to form a bivalent binding (BB) aptamer-cDNA probe. This class of BB probe possesses the advantages of less aptamer bases paired to the cDNA bases for quick response rate and good structural stability for high sensor sensitivity. By use of the rationally designed BB aptamer-cDNA probe, a TISD based EA sensor against ATP with significantly enhanced response rate (with a displacement equilibrium time of 4min) and high sensitivity was successfully constructed. We believe that our BB probe conception will help guide future designs and applications of TISD based EA sensors.
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Affiliation(s)
- Ziping Zhang
- College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Cancan Tao
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - Jungang Yin
- College of Life Sciences, Yantai University, Yantai 264005, China.
| | - Yunhui Wang
- School of Mathematics and Information Sciences, Yantai University, Yantai 264005, China
| | - Yanshen Li
- College of Life Sciences, Yantai University, Yantai 264005, China
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36
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Wang Y, An R, Luo Z, Ye D. Firefly Luciferin-Inspired Biocompatible Chemistry for Protein Labeling and In Vivo Imaging. Chemistry 2017; 24:5707-5722. [PMID: 29068109 DOI: 10.1002/chem.201704349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 12/27/2022]
Abstract
Biocompatible reactions have emerged as versatile tools to build various molecular imaging probes that hold great promise for the detection of biological processes in vitro and/or in vivo. In this Minireview, we describe the recent advances in the development of a firefly luciferin-inspired biocompatible reaction between cyanobenzothiazole (CBT) and cysteine (Cys), and highlight its versatility to label proteins and build multimodality molecular imaging probes. The review starts from the general introduction of biocompatible reactions, which is followed by briefly describing the development of the firefly luciferin-inspired biocompatible chemistry. We then discuss its applications for the specific protein labeling and for the development of multimodality imaging probes (fluorescence, bioluminescence, MRI, PET, photoacoustic, etc.) that enable high sensitivity and spatial resolution imaging of redox environment, furin and caspase-3/7 activity in living cells and mice. Finally, we offer the conclusions and our perspective on the various and potential applications of this reaction. We hope that this review will contribute to the research of biocompatible reactions for their versatile applications in protein labeling and molecular imaging.
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Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Ruibing An
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Zhiliang Luo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Deju Ye
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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37
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Liu M, Yu X, Chen Z, Yang T, Yang D, Liu Q, Du K, Li B, Wang Z, Li S, Deng Y, He N. Aptamer selection and applications for breast cancer diagnostics and therapy. J Nanobiotechnology 2017; 15:81. [PMID: 29132385 PMCID: PMC5683342 DOI: 10.1186/s12951-017-0311-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
Aptamers are short non-coding, single-stranded oligonucleotides (RNA or DNA) developed through Systematic Evolution of Ligands by Exponential enrichment (SELEX) in vitro. Similar to antibodies, aptamers can bind to specific targets with high affinity, and are considered promising therapeutic agents as they have several advantages over antibodies, including high specificity, stability, and non-immunogenicity. Furthermore, aptamers can be produced at a low cost and easily modified, and are, therefore, called "chemical antibodies". In the past years, a variety of aptamers specifically bound to both breast cancer biomarkers and cells had been selected. Besides, taking advantage of nanomaterials, there were a number of aptamer-nanomaterial conjugates been developed and widely investigated for diagnostics and targeted therapy of breast cancer. In this short review, we first present a systematical review of various aptamer selection methods. Then, various aptamer-based diagnostic and therapeutic strategies of breast cancer were provided. Finally, the current problems, challenges, and future perspectives in the field were thoroughly discussed.
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MESH Headings
- Antibiotics, Antineoplastic/chemistry
- Antibiotics, Antineoplastic/therapeutic use
- Aptamers, Nucleotide/chemical synthesis
- Aptamers, Nucleotide/pharmacokinetics
- Aptamers, Nucleotide/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/diagnosis
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Cell Line, Tumor
- Doxorubicin/chemistry
- Doxorubicin/therapeutic use
- Epithelial Cell Adhesion Molecule/genetics
- Epithelial Cell Adhesion Molecule/metabolism
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression
- Humans
- Ligands
- Molecular Targeted Therapy/methods
- Nanotubes
- Protein Binding
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- SELEX Aptamer Technique
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Affiliation(s)
- Mei Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Xiaocheng Yu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Zhu Chen
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
| | - Tong Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Dandan Yang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Qianqian Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Keke Du
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Bo Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189 People’s Republic of China
| | - Song Li
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
| | - Yan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 People’s Republic of China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou, 412007 People’s Republic of China
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Massey M, Medintz IL, Ancona MG, Algar WR. Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. ACS Sens 2017; 2:1205-1214. [PMID: 28787151 DOI: 10.1021/acssensors.7b00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.
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Affiliation(s)
- Melissa Massey
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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Liu L, Yang K, Zhu X, Liang Y, Chen Y, Fang F, Zhao Q, Zhang L, Zhang Y. Aptamer-immobilized open tubular capillary column to capture circulating tumor cells for proteome analysis. Talanta 2017; 175:189-193. [PMID: 28841977 DOI: 10.1016/j.talanta.2017.07.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
Abstract
Circulating tumor cells hold the key to predicting the prognosis and discovering the therapeutic targets. Herein, we proposed a strategy to develop an aptamer-immobilized open tubular capillary column by which SMMC-7721 human hepatoma cells (SMMC-7721 cells) could be captured with an over 70% of capture efficiency and a 3.0 ± 0.2 of enrichment factor. Owing to the compatibility of the column, the captured cells by the column could be analyzed by LC-MS from protein level and 5 unique proteins of SMMC-7721 cells were identified which could be used as markers to identify SMMC-7721 cells when Jurkat T-leukemia cells (Jurkat cells) were employed as interfering cells. As the key component, the aptamer-immobilized column had the potential to be integrated into the platform for separating, enriching and characterizing rare cells simultaneously.
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Affiliation(s)
- Lukuan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xudong Zhu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuanbo Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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40
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Tang J, Yu Y, Shi H, He X, Lei Y, Shangguan J, Yang X, Qiao Z, Wang K. Polyvalent and Thermosensitive DNA Nanoensembles for Cancer Cell Detection and Manipulation. Anal Chem 2017; 89:6637-6644. [DOI: 10.1021/acs.analchem.7b00864] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jinlu Tang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Yanru Yu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Jingfang Shangguan
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Xue Yang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Zhenzhen Qiao
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology
and Molecular Engineering of Hunan Province, Changsha, Hunan 410082, China
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41
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Zhu YJ, Li WJ, Hong ZY, Tang AN, Kong DM. Stable, polyvalent aptamer-conjugated near-infrared fluorescent nanocomposite for high-performance cancer cell-targeted imaging and therapy. J Mater Chem B 2017; 5:9229-9237. [DOI: 10.1039/c7tb02218b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel nanocomposite with improved biostability has been designed and used for cancer cell-specific imaging and targeted therapy.
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Affiliation(s)
- Yan-Jun Zhu
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
| | - Wen-Jing Li
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- P. R. China
- College of Life Science
| | - Zhang-Yong Hong
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- P. R. China
- College of Life Science
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
- Tianjin
- P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
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42
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Zhou Q, Lin Y, Lu M, Tang D. Bismuth ferrite-based photoactive materials for the photoelectrochemical detection of disease biomarkers coupled with multifunctional mesoporous silica nanoparticles. J Mater Chem B 2017; 5:9600-9607. [DOI: 10.1039/c7tb02354e] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A photoelectrochemical sensing system was designed to detect CEA on bismuth ferrite photoactive materials with target-controlled glucose release from mesoporous silica nanoparticles.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Analytic Science for Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Collaborative Innovation Center of Detection Technology for Haixi Food Safety and Products (Fujian Province)
- Department of Chemistry
- Fuzhou University
| | - Youxiu Lin
- Key Laboratory of Analytic Science for Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Collaborative Innovation Center of Detection Technology for Haixi Food Safety and Products (Fujian Province)
- Department of Chemistry
- Fuzhou University
| | - Minghua Lu
- Institute of Environmental and Analytical Science
- School of Chemistry and Chemical Engineering
- Henan University
- Kaifeng 475004
- P. R. China
| | - Dianping Tang
- Key Laboratory of Analytic Science for Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Collaborative Innovation Center of Detection Technology for Haixi Food Safety and Products (Fujian Province)
- Department of Chemistry
- Fuzhou University
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43
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Li B, Li C. Suppression of Prostate Cancer Metastasis by DPYSL3-Targeted saRNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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44
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Béziat V, Hilton HG, Norman PJ, Traherne JA. Deciphering the killer-cell immunoglobulin-like receptor system at super-resolution for natural killer and T-cell biology. Immunology 2016; 150:248-264. [PMID: 27779741 PMCID: PMC5290243 DOI: 10.1111/imm.12684] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Killer-cell immunoglobulin-like receptors (KIRs) are components of two fundamental biological systems essential for human health and survival. First, they contribute to host immune responses, both innate and adaptive, through their expression by natural killer cells and T cells. Second, KIR play a key role in regulating placentation, and hence reproductive success. Analogous to the diversity of their human leucocyte antigen class I ligands, KIR are extremely polymorphic. In this review, we describe recent developments, fuelled by methodological advances, that are helping to decipher the KIR system in terms of haplotypes, polymorphisms, expression patterns and their ligand interactions. These developments are delivering deeper insight into the relevance of KIR in immune system function, evolution and disease.
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Affiliation(s)
- Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
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Parlea L, Puri A, Kasprzak W, Bindewald E, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA. Cellular Delivery of RNA Nanoparticles. ACS COMBINATORIAL SCIENCE 2016; 18:527-47. [PMID: 27509068 PMCID: PMC6345529 DOI: 10.1021/acscombsci.6b00073] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
RNA nanostructures can be programmed to exhibit defined sizes, shapes and stoichiometries from naturally occurring or de novo designed RNA motifs. These constructs can be used as scaffolds to attach functional moieties, such as ligand binding motifs or gene expression regulators, for nanobiology applications. This review is focused on four areas of importance to RNA nanotechnology: the types of RNAs of particular interest for nanobiology, the assembly of RNA nanoconstructs, the challenges of cellular delivery of RNAs in vivo, and the delivery carriers that aid in the matter. The available strategies for the design of nucleic acid nanostructures, as well as for formulation of their carriers, make RNA nanotechnology an important tool in both basic research and applied biomedical science.
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Affiliation(s)
- Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Anu Puri
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Paul Zakrevsky
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily Satterwhite
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kenya Joseph
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte North Carolina 28223, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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