1
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Almeida-Pinto J, Lagarto MR, Lavrador P, Mano JF, Gaspar VM. Cell Surface Engineering Tools for Programming Living Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304040. [PMID: 37823678 DOI: 10.1002/advs.202304040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/10/2023] [Indexed: 10/13/2023]
Abstract
Breakthroughs in precision cell surface engineering tools are supporting the rapid development of programmable living assemblies with valuable features for tackling complex biological problems. Herein, the authors overview the most recent technological advances in chemically- and biologically-driven toolboxes for engineering mammalian cell surfaces and triggering their assembly into living architectures. A particular focus is given to surface engineering technologies for enabling biomimetic cell-cell social interactions and multicellular cell-sorting events. Further advancements in cell surface modification technologies may expand the currently available bioengineering toolset and unlock a new generation of personalized cell therapeutics with clinically relevant biofunctionalities. The combination of state-of-the-art cell surface modifications with advanced biofabrication technologies is envisioned to contribute toward generating living materials with increasing tissue/organ-mimetic bioactivities and therapeutic potential.
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Affiliation(s)
- José Almeida-Pinto
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Matilde R Lagarto
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Pedro Lavrador
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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2
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Qu H, Zheng M, Ma Q, Wang L, Mao Y, Eisenstein M, Tom Soh H, Zheng L. Allosteric Regulation of Aptamer Affinity through Mechano-Chemical Coupling. Angew Chem Int Ed Engl 2023; 62:e202214045. [PMID: 36646642 DOI: 10.1002/anie.202214045] [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: 09/22/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
The capacity to precisely modulate aptamer affinity is important for a wide variety of applications. However, most such engineering strategies entail laborious trial-and-error testing or require prior knowledge of an aptamer's structure and ligand-binding domain. We describe here a simple and generalizable strategy for allosteric modulation of aptamer affinity by employing a double-stranded molecular clamp that destabilizes aptamer secondary structure through mechanical tension. We demonstrate the effectiveness of the approach with a thrombin-binding aptamer and show that we can alter its affinity by as much as 65-fold. We also show that this modulation can be rendered reversible by introducing a restriction enzyme cleavage site into the molecular clamp domain and describe a design strategy for achieving even more finely-tuned affinity modulation. This strategy requires no prior knowledge of the aptamer's structure and binding mechanism and should thus be generalizable across aptamers.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Manyi Zheng
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Qihui Ma
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Lu Wang
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Yu Mao
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Michael Eisenstein
- Department of Electrical Engineering and Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Hyongsok Tom Soh
- Department of Electrical Engineering and Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Lei Zheng
- School of Food and Biological Engineering and Engineering Research Center of Bioprocess of Ministry of Education, Hefei University of Technology, Hefei, 230009, China
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3
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Liu Q, Huang Y, Li L, Li Z, Li M. Endogenous Enzyme-Operated Spherical Nucleic Acids for Cell-Selective Protein Capture and Localization Regulation. Angew Chem Int Ed Engl 2023; 62:e202214958. [PMID: 36788111 DOI: 10.1002/anie.202214958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/16/2023]
Abstract
Precise regulation of protein activity and localization in cancer cells is crucial to dissect the function of the protein-involved cellular network in tumorigenesis, but there is a lack of suitable methodology. Here we report the design of enzyme-operated spherical nucleic acids (E-SNAs) for manipulation of the nucleocytoplasmic translocation of proteins with cancer-cell selectivity. The E-SNAs are constructed by programmable engineering of aptamer-based modules bearing enzyme-responsive units in predesigned sites and further combination with SNA nanotechnology. We demonstrate that E-SNAs are able to regulate cytoplasmic-to-nuclear shuttling of RelA protein efficiently and specifically in tumor cells, while they remain inactive in normal cells due to insufficient enzyme expression. We further confirmed the generality of this strategy by investigating the enzyme-modulated inhibition/activation of thrombin activity by varying the aptamer-based design.
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Affiliation(s)
- Qing Liu
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
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4
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de Moliner F, Konieczna Z, Mendive-Tapia L, Saleeb RS, Morris K, Gonzalez-Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. Angew Chem Int Ed Engl 2023; 62:e202216231. [PMID: 36412996 PMCID: PMC10108274 DOI: 10.1002/anie.202216231] [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: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
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Affiliation(s)
- Fabio de Moliner
- Centre for Inflammation Research, The University of Edinburgh, UK
| | | | | | | | - Katie Morris
- EaStCHEM School of Chemistry, The University of Edinburgh, UK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | | | - Marc Vendrell
- Centre for Inflammation Research, The University of Edinburgh, UK
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5
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de Moliner F, Konieczna Z, Mendive‐Tapia L, Saleeb RS, Morris K, Gonzalez‐Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202216231. [PMID: 38515539 PMCID: PMC10952862 DOI: 10.1002/ange.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
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Affiliation(s)
| | | | | | | | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain SciencesThe University of EdinburghUK
| | | | | | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghUK
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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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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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8
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Akiyama M, Ueki R, Yanagawa M, Abe M, Hiroshima M, Sako Y, Sando S. DNA‐Based Synthetic Growth Factor Surrogates with Fine‐Tuned Agonism**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Momoko Akiyama
- Department of Chemistry and Biotechnology The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Michio Hiroshima
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Laboratory for Cell Signaling Dynamics RIKEN Center for, Biosystems Dynamics Research 6-2-3, Furuedai, Suita Osaka 565-0874 Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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9
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Akiyama M, Ueki R, Yanagawa M, Abe M, Hiroshima M, Sako Y, Sando S. DNA-Based Synthetic Growth Factor Surrogates with Fine-Tuned Agonism*. Angew Chem Int Ed Engl 2021; 60:22745-22752. [PMID: 34142433 DOI: 10.1002/anie.202105314] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/16/2021] [Indexed: 11/06/2022]
Abstract
Designing synthetic surrogates of functional proteins is an important, albeit challenging, task in the field of chemistry. A strategy toward the design of synthetic agonists for growth factor or cytokine receptors that elicit a desired signal activity has been in high demand, as such ligands hold great promise as safer and more effective therapeutics. In the present study, we used a DNA aptamer as a building block and described the strategy-guided design of a synthetic receptor agonist with fine-tuned agonism. The developed synthetic partial agonist can regulate therapeutically relevant cellular activities by eliciting fine-tuned receptor signaling.
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Affiliation(s)
- Momoko Akiyama
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Michio Hiroshima
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Laboratory for Cell Signaling Dynamics, RIKEN Center for, Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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10
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Xue J, Chen F, Bai M, Cao X, Fu W, Zhang J, Zhao Y. Aptamer-Functionalized Microdevices for Bioanalysis. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9402-9411. [PMID: 33170621 DOI: 10.1021/acsami.0c16138] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aptamers have drawn great attention in the field of biological research and disease diagnosis for the remarkable advantages as recognition elements. They show unique superiority for facile selection, desirable thermal stability, flexible engineering, and low immunogenicity, complementing the use of conventional antibodies. Aptamer-functionalized microdevices offer promising properties for bioanalysis applications because of the compact sizes, minimal reaction volume, high throughput, operational feasibility, and controlled preciseness. In this review, we first introduce the innovative technologies in the selection of aptamers with microdevices and then highlight some advanced applications of aptamer-functionalized microdevices in bioanalysis field for diverse targets. Aptamer-functionalized microfluidic devices, microarrays, and paper-based and other interface-based microdevices are all bioanalysis platforms with huge potential in the near future. Finally, the major challenges of these microdevices applied in bioanalysis are discussed and future perspectives are also envisioned.
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Affiliation(s)
- Jing Xue
- 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - Min Bai
- 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - Xiaowen Cao
- 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - Wenhao Fu
- 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - Jin Zhang
- 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - 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, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
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