1
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Liu Y, Zhao Z, Zeng Y, He M, Lyu Y, Yuan Q. Thermodynamics and Kinetics-Directed Regulation of Nucleic Acid-Based Molecular Recognition. SMALL METHODS 2024:e2401102. [PMID: 39392199 DOI: 10.1002/smtd.202401102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/28/2024] [Indexed: 10/12/2024]
Abstract
Nucleic acid-based molecular recognition plays crucial roles in various fields like biosensing and disease diagnostics. To achieve optimal detection and analysis, it is essential to regulate the response performance of nucleic acid probes or switches to match specific application requirements by regulating thermodynamics and kinetics properties. However, the impacts of thermodynamics and kinetics theories on recognition performance are sometimes obscure and the relative conclusions are not intuitive. To promote the thorough understanding and rational utilization of thermodynamics and kinetics theories, this review focuses on the landmarks and recent advances of nucleic acid thermodynamics and kinetics and summarizes the nucleic acid thermodynamics and kinetics-based strategies for regulation of nucleic acid-based molecular recognition. This work hopes such a review can provide reference and guidance for the development and optimization of nucleic acid probes and switches in the future, as well as for advancements in other nucleic acid-related fields.
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Affiliation(s)
- Yihao Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Zihan Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Minze He
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
- Furong Laboratory, Changsha, 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
- Institute of Chemical Biology and Nanomedicine, College of Biology, Hunan University, Changsha, 410082, China
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2
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Ouyang Y, Zhang P, Willner I. DNA Tetrahedra as Functional Nanostructures: From Basic Principles to Applications. Angew Chem Int Ed Engl 2024; 63:e202411118. [PMID: 39037936 DOI: 10.1002/anie.202411118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 07/24/2024]
Abstract
Self-assembled supramolecular DNA tetrahedra composed of programmed sequence-engineered complementary base-paired strands represent elusive nanostructures having key contributions to the development and diverse applications of DNA nanotechnology. By appropriate engineering of the strands, DNA tetrahedra of tuneable sizes and chemical functionalities were designed. Programmed functionalities for diverse applications were integrated into tetrahedra structures including sequence-specific recognition strands (aptamers), catalytic DNAzymes, nanoparticles, proteins, or fluorophore. The article presents a comprehensive review addressing methods to assemble and characterize the DNA tetrahedra nanostructures, and diverse applications of DNA tetrahedra framework are discussed. Topics being addressed include the application of structurally functionalized DNA tetrahedra nanostructure for the assembly of diverse optical or electrochemical sensing platforms and functionalized intracellular sensing and imaging modules. In addition, the triggered reconfiguration of DNA tetrahedra nanostructures and dynamic networks and circuits emulating biological transformations are introduced. Moreover, the functionalization of DNA tetrahedra frameworks with nanoparticles provides building units for the assembly of optical devices and for the programmed crystallization of nanoparticle superlattices. Finally, diverse applications of DNA tetrahedra in the field of nanomedicine are addressed. These include the DNA tetrahedra-assisted permeation of nanocarriers into cells for imaging, controlled drug release, active chemodynamic/photodynamic treatment of target tissues, and regenerative medicine.
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Affiliation(s)
- Yu Ouyang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Pu Zhang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Current address: Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P.R. China
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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3
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Armero L, Plou J, Valera PS, Serna S, García I, Liz-Marzán LM. Multiplex Determination of Glycan Profiles on Urinary Prostate-Specific Antigen by Quartz-Crystal Microbalance Combined with Surface-Enhanced Raman Scattering. ACS Sens 2024; 9:4811-4821. [PMID: 39213515 PMCID: PMC11443522 DOI: 10.1021/acssensors.4c01252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Prostate cancer remains a major health concern, with prostate-specific antigen (PSA) being a key biomarker for its detection and monitoring. However, PSA levels often fall into a "gray zone", where PSA levels are not clearly indicative of cancer, thus complicating early diagnosis and treatment decisions. Glycosylation profiles, which often differ between healthy and diseased cells, have emerged as potential biomarkers to enhance the specificity and sensitivity of cancer diagnosis in these ambiguous cases. We propose the integration of two complementary techniques, namely quartz-crystal microbalance with dissipation (QCM-D) and surface-enhanced Raman scattering (SERS) to study PSA glycan profiles. QCM-D offers real-time operation, PSA mass quantification, and label-free detection with high sensitivity, as well as enhanced specificity and reduced cross-reactivity when using nucleic acid aptamers as capture ligands. Complementary SERS sensing enables the determination of the glycosylation pattern on PSA, at low concentrations and without the drawbacks of photobleaching, thereby facilitating multiplexed glycosylation pattern analysis. This integrated setup could retrieve a data set comprising analyte concentrations and associated glycan profiles in relevant biological samples, which may eventually improve early disease detection and monitoring. Prostate-specific antigen (PSA), a glycoprotein secreted by prostate epithelial cells, serves as our proof-of-concept analyte. Our platform allows multiplex targeting of PSA multiplex glycosylation profiles of PSA at "gray zone" concentrations for prostate cancer diagnosis. We additionally show the use of SERS for glycan analysis in PSA secreted from prostate cancer cell lines after androgen-based treatment. Differences in PSA glycan profiles from resistant cell lines after androgen-based treatment may eventually improve cancer treatment.
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Affiliation(s)
- Laura Armero
- CIC
biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Department
of Applied Chemistry, University of the
Basque Country, Donostia-San Sebastián 20018, Spain
| | - Javier Plou
- CIC
biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- CIC
nanoGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20018, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine
(CIBER-BBN), Donostia-San Sebastián 20014, Spain
| | - Pablo S. Valera
- CIC
biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Department
of Applied Chemistry, University of the
Basque Country, Donostia-San Sebastián 20018, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine
(CIBER-BBN), Donostia-San Sebastián 20014, Spain
- CIC
bioGUNE, Basque Research and Technology Alliance (BRTA), Derio 48160, Spain
| | - Sonia Serna
- CIC
biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
| | - Isabel García
- CIC
biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine
(CIBER-BBN), Donostia-San Sebastián 20014, Spain
| | - Luis M. Liz-Marzán
- CIC
biomaGUNE, Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián 20014, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine
(CIBER-BBN), Donostia-San Sebastián 20014, Spain
- IKERBASQUE,
Basque Foundation for Science, Bilbao 48009, Spain
- Cinbio, Universidade de Vigo, Vigo 36310, Spain
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4
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Wang C, Zhang J, Pei Y, Li C, Li Y, Chen S, Wang Z. Visualized electrochemiluminescence detection of trace copper in practical food samples. Food Chem 2024; 451:139461. [PMID: 38701733 DOI: 10.1016/j.foodchem.2024.139461] [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: 02/04/2024] [Revised: 04/09/2024] [Accepted: 04/21/2024] [Indexed: 05/05/2024]
Abstract
Copper as a widely applied element in food supply chain can cause serious contamination issues that threats food safety. In this research, we present a quick and visible method for trace copper ion (Cu2+) quantification in practical food samples. Polymer dots (Pdots) were firstly conjugated with a copper-specific DNA aptamer and then tailored with rhodamine B (RhB) to extinguish the electrochemiluminescence (ECL) signal through a resonance energy transfer process. The selective release of RhB leads to signal restoration when exposed to trace Cu2+ levels, achieving remarkable linearity with the logarithm of Cu2+ concentration within the range of 1 ng/L to 10 μg/L with an impressively low limit of detection at 11.8 pg/L. Most notably, our device was also applicable on visualizing and quantifying trace Cu2+ (∼0.2 μg/g) in practical Glycyrrhiza uralensis Fisch. samples, underscoring its potential as a tool for the early prevention of potential copper contamination in food samples.
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Affiliation(s)
- Cheng Wang
- School of Pharmacy, Changzhou University, No. 21 Middle Gehu Road, Changzhou 213164, PR China.
| | - Jiaxing Zhang
- School of Pharmacy, Changzhou University, No. 21 Middle Gehu Road, Changzhou 213164, PR China
| | - Yang Pei
- Chinese Cultural Teaching Centre, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou 215123, PR China
| | - Chengqi Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, PR China
| | - Yulin Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, PR China
| | - Shaoqing Chen
- Department of Radiology, Second People's Hospital of Changzhou, Nanjing Medical University, Changzhou 213004, PR China.
| | - Ziyu Wang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, PR China.
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5
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Ogunmolasuyi AM, Adewoyin MA. Microfluidic device: A versatile biosensor platform to multiplex aptamer-based detection of malaria biomarkers. Cell Biochem Funct 2024; 42:e4104. [PMID: 39118353 DOI: 10.1002/cbf.4104] [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: 03/23/2024] [Revised: 07/03/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
Plasmodium falciparum malaria remains a dominant infectious disease that affects Africa than the rest of the world, considering its associated cases and death rates. It's a febrile illness that produces several reliable biomarkers, for example, P. falciparum lactate dehydrogenase (PfLDH), P. falciparum Plasmodium glutamate dehydrogenase (PfGDH), and P. falciparum histidine-rich proteins (HRP-II) in blood circulatory system that can easily be employed as targets in rapid diagnostic tests (RDTs). In recent times, several DNA aptamers have been developed via SELEX technology to detect some specific malaria biomarkers (PfLDH, PvLDH, HRP-II, PfGDH) in a biosensor mode with good binding affinity properties to overcome the trend of cross-reactivity, limited sensitivity and stability problems that have been observed with immunodiagnostics. In this review, we summarized existing diagnostic methods and relevant biomarkers to suggest promising approaches to develop sensitive and species-specific multiplexed diagnostic devices enabling effective detection of malaria in complex biological matrices and surveillance in the endemic region.
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Affiliation(s)
| | - Mary A Adewoyin
- Department of Biological Sciences, Anchor University, Lagos, Nigeria
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6
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
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7
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Duhan J, Kumar H, Obrai S. Recent Advances in Nanomaterials Based Optical Sensors for the Detection of Melatonin and Serotonin. J Fluoresc 2024:10.1007/s10895-024-03647-3. [PMID: 38436821 DOI: 10.1007/s10895-024-03647-3] [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: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
In this review paper we discussed the detection of melatonin and serotonin by using various optical methods. Melatonin and serotonin are very necessary body hormones these are also called neuroregulatory hormones secreted by pineal gland in brain by pinealocytes and shape of pineal gland is cone like. Sensitive detection of melatonin and serotonin in pharmacological samples and human serum is crucial for human beings, lots of research publications available in literature for melatonin and serotonin and we overviewed these papers. We have deeply reviewed many research papers where sensitively sensing of melatonin and serotonin occurs, by using of various interfering agents and nanomaterials. This review aims presenting colorimetry, fluorometry and spectrophotometric detection of melatonin (MEL) and serotonin (SER) by using different metal oxides, carbon nanomaterials (nanosheets, nanorods, nanofibers) and many other agents. Nanomaterials typically possess favourable optical, electrical and mechanical characteristics, they provide up new avenues for enhancing the efficacy of sensors. It is crucial to provide an optical sensors platform that is dependable, sensitive and low price. The development of sensors and biosensors to use nanomaterials for neurotransmitters has advanced significantly in recent years. There are currently many developing biomarkers in biological fluids, and bionanomaterial-based biosensor systems, as well as clinical and pharmacological settings, have garnered significant interest. Biomarkers have been found using optical devices in a quick, selective and sensitive manner. Our aim is to compile all the data that already published on MEL, SER sensing and comparison of each method, we mainly focused on principle, observations, sensitivity, selectivity, limit of detection, mechanism behind the reaction, effect of temperature, pH and concentration. In the last of this paper, we discuss some challenges of these methods and future projects.
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Affiliation(s)
- Jyoti Duhan
- Dr BR Ambedkar national institute of technology, Jalandhar, Punjab, India
| | - Himanshu Kumar
- Dr BR Ambedkar national institute of technology, Jalandhar, Punjab, India
| | - Sangeeta Obrai
- Dr BR Ambedkar national institute of technology, Jalandhar, Punjab, India.
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8
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Ouyang Y, O'Hagan MP, Willner B, Willner I. Aptamer-Modified Homogeneous Catalysts, Heterogenous Nanoparticle Catalysts, and Photocatalysts: Functional "Nucleoapzymes", "Aptananozymes", and "Photoaptazymes". ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2210885. [PMID: 37083210 DOI: 10.1002/adma.202210885] [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: 11/22/2022] [Revised: 01/18/2023] [Indexed: 05/03/2023]
Abstract
Conjugation of aptamers to homogeneous catalysts ("nucleoapzymes"), heterogeneous nanoparticle catalysts ("aptananozymes"), and photocatalysts ("photoaptazymes") yields superior catalytic/photocatalytic hybrid nanostructures emulating functions of native enzymes and photosystems. The concentration of the substrate in proximity to the catalytic sites ("molarity effect") or spatial concentration of electron-acceptor units in spatial proximity to the photosensitizers, by aptamer-ligand complexes, leads to enhanced catalytic/photocatalytic efficacies of the hybrid nanostructures. This is exemplified by sets of "nucleoapzymes" composed of aptamers conjugated to the hemin/G-quadruplex DNAzymes or metal-ligand complexes as catalysts, catalyzing the oxidation of dopamine to aminochrome, oxygen-insertion into the Ar─H moiety of tyrosinamide and the subsequent oxidation of the catechol product into aminochrome, or the hydrolysis of esters or ATP. Also, aptananozymes consisting of aptamers conjugated to Cu2+ - or Ce4+ -ion-modified C-dots or polyadenine-stabilized Au nanoparticles acting as catalysts oxidizing dopamine or operating bioreactor biocatalytic cascades, are demonstrated. In addition, aptamers conjugated to the Ru(II)-tris-bipyridine photosensitizer or the Zn(II) protoporphyrin IX photosensitizer provide supramolecular photoaptazyme assemblies emulating native photosynthetic reaction centers. Effective photoinduced electron transfer followed by the catalyzed synthesis of NADPH or the evolution of H2 is demonstrated by the photosystems. Structure-function relationships dictate the catalytic and photocatalytic efficacies of the systems.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Michael P O'Hagan
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Bilha Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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9
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Wang X, Kong F, Liu Y, Lv S, Zhang K, Sun S, Liu J, Wang M, Cai X, Jin H, Yan S, Luo J. 17β-estradiol biosensors based on different bioreceptors and their applications. Front Bioeng Biotechnol 2024; 12:1347625. [PMID: 38357703 PMCID: PMC10864596 DOI: 10.3389/fbioe.2024.1347625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
17β-Estradiol (E2) is a critical sex steroid hormone, which has significant effects on the endocrine systems of both humans and animals. E2 is also believed to play neurotrophic and neuroprotective roles in the brain. Biosensors present a powerful tool to detect E2 because of their small, efficient, and flexible design. Furthermore, Biosensors can quickly and accurately obtain detection results with only a small sampling amount, which greatly meets the detection of the environment, food safety, medicine safety, and human body. This review focuses on previous studies of biosensors for detecting E2 and divides them into non-biometric sensors, enzyme biosensors, antibody biosensors, and aptamer biosensors according to different bioreceptors. The advantages, disadvantages, and design points of various bioreceptors for E2 detection are analyzed and summarized. Additionally, applications of different bioreceptors of E2 detection are presented and highlight the field of environmental monitoring, food and medicine safety, and disease detection in recent years. Finally, the development of E2 detection by biosensor is prospected.
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Affiliation(s)
- Xinyi Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Fanli Kong
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yaoyao Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Shiya Lv
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Kui Zhang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Shutong Sun
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Juntao Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Mixia Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Xinxia Cai
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Jin
- Obstetrics and Gynecology Department, Peking University First Hospital, Beijing, China
| | - Shi Yan
- Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinping Luo
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing, China
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10
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Wang Y, Duan H, Yalikun Y, Cheng S, Li M. A pendulum-type electrochemical aptamer-based sensor for continuous, real-time and stable detection of proteins. Talanta 2024; 266:125026. [PMID: 37544252 DOI: 10.1016/j.talanta.2023.125026] [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: 04/24/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
Continuous detection of proteins is crucial for health management and biomedical research. Electrochemical aptamer-based (E-AB) sensor that relies on binding affinity between a recognition oligonucleotide and its specific target is a versatile platform to fulfill this purpose. Yet, the vast majority of E-AB sensors are characterized by voltammetric methods, which suffer from signal drifts and low-frequency data acquisition during continuous operations. To overcome these limitations, we developed a novel E-AB sensor empowered by Gold nanoparticle-DNA Pendulum (GDP). Using chronoamperometric interrogation, the developed sensor enabled drift-resistant, high-frequency, and real-time monitoring of vascular endothelial growth factor (VEGF), a vital signaling protein that regulates angiogenesis, endothelial cell proliferation and vasculogenesis. We assembled VEGF aptamer-anchored GDP probes to a reduced graphene modified electrode, where a fast chronoamperometric current transient occurs as the GDP rapidly transport to the electrode surface. In the presence of target molecules, longer and concentration-dependent time decays were observed because of slower motion of the GDP in its bound state. After optimizing several decisive parameters, including composition ratios of GDP, probe density, and incubation time, the GDP empowered E-AB sensor achieves continuous, selective, and reversible monitoring of VEGF in both phosphate buffered saline (PBS) solutions and artificial urine with a wide detection range from 13 fM to 130 nM. Moreover, the developed sensor acquires signals on a millisecond timescale, and remains resistant to signal degradation during operation. This study offers a new approach to designing E-AB architectures for continuous biomolecular monitoring.
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Affiliation(s)
- Yizhou Wang
- School of Engineering, Macquarie University, Sydney, 2109, NSW, Australia
| | - Haowei Duan
- School of Engineering, Macquarie University, Sydney, 2109, NSW, Australia
| | - Yaxiaer Yalikun
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Shaokoon Cheng
- School of Engineering, Macquarie University, Sydney, 2109, NSW, Australia
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, 2109, NSW, Australia.
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11
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O’Hagan M, Duan Z, Huang F, Laps S, Dong J, Xia F, Willner I. Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications. Chem Rev 2023; 123:6839-6887. [PMID: 37078690 PMCID: PMC10214457 DOI: 10.1021/acs.chemrev.3c00016] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/21/2023]
Abstract
This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.
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Affiliation(s)
- Michael
P. O’Hagan
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Shay Laps
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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12
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Nagano M, Toda T, Makino K, Miki H, Sugizaki Y, Tomizawa H, Isobayashi A, Yoshimoto K. Discovery of a Highly Specific Anti-methotrexate (MTX) DNA Aptamer for Antibody-Independent MTX Detection. Anal Chem 2022; 94:17255-17262. [PMID: 36449359 DOI: 10.1021/acs.analchem.2c04182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
High-dose methotrexate (MTX) therapy is used to treat a wide variety of cancers such as leukemia and lymphoma, while the resulting high blood concentration of MTX faces a risk of life-threatening side effects, so it is essential to monitor the concentration carefully. Currently, the MTX concentration is measured using antibody-based kits in a clinical setting; however, the heterogeneity and batch-to-batch variation of antibodies potentially compromise the detection limit. Here, we developed MTX detection systems with chemically synthesizable homogeneous oligonucleotides. Microbead-assisted capillary electrophoresis (MACE)-SELEX against MTX successfully identified MSmt7 with a similar level of specificity to anti-MTX antibodies within three rounds. The 3'-end of MSmt7 was coupled to a peroxidase-like hemin-DNAzyme to construct a bifunctional oligonucleotide for MTX sensing, where MTX in 50% human serum was detected with a limit of detection (LoD) of 118 nM. Furthermore, amplifying the DNAzyme region with rolling circle amplification significantly improved the sensitivity with an LoD of 290 pM. Presented oligonucleotide-based MTX detection systems will pave the way for antibody-independent MTX detection with reliability and less cost in the laboratory and the clinic.
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Affiliation(s)
- Masanobu Nagano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takumi Toda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Kurumi Makino
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Hiroko Miki
- Corporate Research & Development Center, Toshiba Corporation, Kanagawa 212-8582, Japan
| | - Yoshiaki Sugizaki
- Corporate Research & Development Center, Toshiba Corporation, Kanagawa 212-8582, Japan
| | - Hideyuki Tomizawa
- Corporate Research & Development Center, Toshiba Corporation, Kanagawa 212-8582, Japan
| | - Atsunobu Isobayashi
- Corporate Research & Development Center, Toshiba Corporation, Kanagawa 212-8582, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
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13
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Schmitz FRW, Cesca K, Valério A, de Oliveira D, Hotza D. Colorimetric detection of Pseudomonas aeruginosa by aptamer-functionalized gold nanoparticles. Appl Microbiol Biotechnol 2022; 107:71-80. [DOI: 10.1007/s00253-022-12283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022]
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14
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Zhu X, Tang J, Ouyang X, Liao Y, Feng H, Yu J, Chen L, Lu Y, Yi Y, Tang L. Hollow NiCo@C Nanozyme-Embedded Paper-Based Colorimetric Aptasensor for Highly Sensitive Antibiotic Detection on a Smartphone Platform. Anal Chem 2022; 94:16768-16777. [DOI: 10.1021/acs.analchem.2c03603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Xu Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Jing Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Xilian Ouyang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Yibo Liao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Haopeng Feng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Jiangfang Yu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Li Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Yating Lu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Yuyang Yi
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, Hunan, China
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15
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Fadeev M, O’Hagan MP, Biniuri Y, Willner I. Aptamer-Protein Structures Guide In Silico and Experimental Discovery of Aptamer-Short Peptide Recognition Complexes or Aptamer-Amino Acid Cluster Complexes. J Phys Chem B 2022; 126:8931-8939. [PMID: 36315022 PMCID: PMC9661473 DOI: 10.1021/acs.jpcb.2c05624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence participating in the binding of the protein to the aptamer. The subsequent fragmentation of the peptide sequence into short peptides and the in silico docking-guided identification of affinity complexes between the miniaturized peptides and the antiprotein aptamer, followed by experimental validation of the binding features of the short peptides with the antiprotein aptamers, leads to the identification of new short peptide-aptamer complexes. This is exemplified with the identification of the pentapeptide RYERN as the scaffold that binds thrombin to the DNA thrombin aptamer (DNA TA). In silico docking studies followed by microscale thermophoresis (MST) experiments demonstrate that the miniaturized tripeptides RYE, YER, and ERN reveal selective binding affinities toward the DNA TA. In addition, docking and MST experiments show that the ribonucleotide-translated RNA TA shows related binding affinities of YER to the DNA TA. Most importantly, we demonstrate that the separated amino acids Y/E/R assemble as a three amino acid cluster on the DNA TA and RNA TA aptamers in spatial configurations similar to the tripeptide YER on the respective aptamers. The clustering phenomenon is selective for the YER tripeptide system. The method to identify binding affinities of miniaturized peptides to known antiprotein aptamers and the specific clustering of single amino acids on the aptamers is further demonstrated by in silico and experimental identification of the binding of the tripeptide RET and the selective clustering of the separated amino acids R/E/T onto a derivative of the AS1411 aptamer against the nucleolin receptor protein.
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16
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Karthik V, Karuna B, Kumar PS, Saravanan A, Hemavathy RV. Development of lab-on-chip biosensor for the detection of toxic heavy metals: A review. CHEMOSPHERE 2022; 299:134427. [PMID: 35358561 DOI: 10.1016/j.chemosphere.2022.134427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Recently, a decrease in water availability and quality has been raised due to rapid industrialization, unsustainable agricultural activities and anthropogenic activities. Heavy metals are considered significant pollutants in the water environment, cause environmental hazards and health effects to humans. For monitoring water contaminants utilized different conventional techniques. Still, they have some drawbacks, such as cost expensive, ecological issues, and processing time, requiring technicians and researchers to operate them effectively. Biosensors have become reasonable devices for screening and identifying environmental contaminants because of their different benefits contrasted with other detecting techniques. This review summarizes the toxic effect of heavy metal and their source, occurrence. A detailed discussion is provided on the heavy metal recognition materials for detecting heavy metals in wastewater. Lab on chip (LOC) is an emerging micro-electrical mechanical system (MEMS) device that intakes liquid and makes it move through the micro-channels, to accomplish fast, cost-effective and profoundly sensitive analysis with significant yield. LOC also provided a discussion on numerous laboratory functions on a single platform. This article attempts to discuss the detection of heavy metals using lab on a chip by suitable recognition materials. Further, the design and fabrication mechanism and their recognition abilities of LOC were also reviewed. The review mainly focuses on the application of LOC biosensors, pros, and cons, and suggests a roadmap towards future development to enhance the practical use in pollutant monitoring.
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Affiliation(s)
- V Karthik
- Department of Industrial Biotechnology, Government College of Technology, Coimbatore, India
| | - B Karuna
- Department of Industrial Biotechnology, Government College of Technology, Coimbatore, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
| | - A Saravanan
- Department of Energy and Environmental Engineering, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - R V Hemavathy
- Department of Biotechnology, Rajalakshmi Engineering College, Chennai, 602105, India
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17
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Zhang J, Lan T, Lu Y. Overcoming Major Barriers to Developing Successful Sensors for Practical Applications Using Functional Nucleic Acids. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:151-171. [PMID: 35216531 PMCID: PMC9197978 DOI: 10.1146/annurev-anchem-061020-104216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
For many years, numerous efforts have been focused on the development of sensitive, selective, and practical sensors for environmental monitoring, food safety, and medical diagnostic applications. However, the transition from innovative research to commercial success is relatively sparse. In this review, we identify four scientific barriers and one technical barrier to developing successful sensors for practical applications, including the lack of general methods to (a) generate receptors for a wide range of targets, (b) improve sensor selectivity to overcome interferences, (c) transduce the selective binding to different optical, electrochemical, and other signals, and (d) tune dynamic range to match thresholds of detection required for different targets; and the costly development of a new device. We then summarize solutions to overcome these barriers using sensors based on functional nucleic acids that include DNAzymes, aptamers, and aptazymes and how these sensors are coupled to widely available measurement devices to expand their capabilities and lower the barrier for their practical applications in the field and point-of-care settings.
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Affiliation(s)
- JingJing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China;
| | - Tian Lan
- GlucoSentient, Inc., Champaign, Illinois, USA
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
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18
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Tang T, Liu Y, Jiang Y. Recent Progress on Highly Selective and Sensitive Electrochemical Aptamer-based Sensors. Chem Res Chin Univ 2022; 38:866-878. [PMID: 35530120 PMCID: PMC9069955 DOI: 10.1007/s40242-022-2084-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/10/2022] [Indexed: 12/31/2022]
Abstract
Highly selective, sensitive, and stable biosensors are essential for the molecular level understanding of many physiological activities and diseases. Electrochemical aptamer-based (E-AB) sensor is an appealing platform for measurement in biological system, attributing to the combined advantages of high selectivity of the aptamer and high sensitivity of electrochemical analysis. This review summarizes the latest development of E-AB sensors, focuses on the modification strategies used in the fabrication of sensors and the sensing strategies for analytes of different sizes in biological system, and then looks forward to the challenges and prospects of the future development of electrochemical aptamer-based sensors.
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Affiliation(s)
- Tianwei Tang
- College of Chemistry, Beijing Normal University, Beijing, 100875 P. R. China
| | - Yinghuan Liu
- College of Chemistry, Beijing Normal University, Beijing, 100875 P. R. China
| | - Ying Jiang
- College of Chemistry, Beijing Normal University, Beijing, 100875 P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing, 100190 P. R. China
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19
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Yang X, Liang X, Nandi R, Tian Y, Zhang Y, Li Y, Zhou J, Dong Y, Liu D, Zhong Z, Yang Z. DNA-Modified Liquid Crystal Droplets. BIOSENSORS 2022; 12:275. [PMID: 35624576 PMCID: PMC9138460 DOI: 10.3390/bios12050275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
In this work, we have combined the advantages of sequence programmability of DNA nanotechnology and optical birefringence of liquid crystals (LCs). Herein, DNA amphiphiles were adsorbed onto LC droplets. A unique phenomenon of LC droplet aggregation was demonstrated, using DNA-modified LC droplets, through complementary DNA hybridization. Further functionalization of DNA-modified LC droplets with a desired DNA sequence was used to detect a wide range of chemicals and biomolecules, such as Hg2+, thrombin, and enzymes, through LC droplet aggregation and vice versa, which can be seen through the naked eye. These DNA-modified LC droplets can be printed onto a desired patterned surface with temperature-induced responsiveness and reversibility. Overall, our work is the first to report DNA-modified LC droplet, which provides a general detection platform based on the development of DNA aptamers. Additionally, this work inspires the exploration of surface information visualization combined with microcontact printing.
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Affiliation(s)
- Xiuxiu Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Xiao Liang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Rajib Nandi
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yi Tian
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yan Li
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Jingsheng Zhou
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Yuanchen Dong
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
| | - Zhengwei Zhong
- Department of Chemical Engineering, Hebei Petroleum University of Technology, Chengde 067000, China
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China; (X.Y.); (X.L.); (R.N.); (Y.T.); (Y.Z.); (Y.L.); (J.Z.); (Y.D.); (D.L.)
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20
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Wang Y, Liu X, Wu L, Ding L, Effah CY, Wu Y, Xiong Y, He L. Construction and bioapplications of aptamer-based dual recognition strategy. Biosens Bioelectron 2022; 195:113661. [PMID: 34592501 DOI: 10.1016/j.bios.2021.113661] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/08/2023]
Abstract
Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.
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Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinlian Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Longjie Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Clement Yaw Effah
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
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21
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Fan Q, Gao Y, Mazur F, Chandrawati R. Nanoparticle-based colorimetric sensors to detect neurodegenerative disease biomarkers. Biomater Sci 2021; 9:6983-7007. [PMID: 34528639 DOI: 10.1039/d1bm01226f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Neurodegenerative disorders (NDDs) are progressive, incurable health conditions that primarily affect brain cells, and result in loss of brain mass and impaired function. Current sensing technologies for NDD detection are limited by high cost, long sample preparation, and/or require skilled personnel. To overcome these limitations, optical sensors, specifically colorimetric sensors, have garnered increasing attention towards the development of a cost-effective, simple, and rapid alternative approach. In this review, we evaluate colorimetric sensing strategies of NDD biomarkers (e.g. proteins, neurotransmitters, bio-thiols, and sulfide), address the limitations and challenges of optical sensor technologies, and provide our outlook on the future of this field.
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Affiliation(s)
- Qingqing Fan
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia.
| | - Yuan Gao
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia.
| | - Federico Mazur
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia.
| | - Rona Chandrawati
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia.
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22
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Liu D, Huang P, Wu FY. Highly Specific and Rapid Colorimetric Detection of Tetracycline in Pills and Milk Based on Aptamer-Controlled Aggregation of Silver Nanoparticles. CHEMISTRY AFRICA 2021. [DOI: 10.1007/s42250-021-00286-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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23
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Ouyang Y, Biniuri Y, Fadeev M, Zhang P, Carmieli R, Vázquez-González M, Willner I. Aptamer-Modified Cu 2+-Functionalized C-Dots: Versatile Means to Improve Nanozyme Activities-"Aptananozymes". J Am Chem Soc 2021; 143:11510-11519. [PMID: 34286967 PMCID: PMC8856595 DOI: 10.1021/jacs.1c03939] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The covalent linkage of aptamer binding
sites to nanoparticle nanozymes
is introduced as a versatile method to improve the catalytic activity
of nanozymes by concentrating the reaction substrates at the catalytic
nanozyme core, thereby emulating the binding and catalytic active-site
functions of native enzymes. The concept is exemplified with the synthesis
of Cu2+ ion-functionalized carbon dots (C-dots), modified
with the dopamine binding aptamer (DBA) or the tyrosinamide binding
aptamer (TBA), for the catalyzed oxidation of dopamine to aminochrome
by H2O2 or the oxygenation of l-tyrosinamide
to the catechol product, which is subsequently oxidized to amidodopachrome,
in the presence of H2O2/ascorbate mixture. Sets
of structurally functionalized DBA-modified Cu2+ ion-functionalized
C-dots or sets of structurally functionalized TBA-modified Cu2+ ion-functionalized C-dots are introduced as nanozymes of
superior catalytic activities (aptananozymes) toward the oxidation
of dopamine or the oxygenation of l-tyrosinamide, respectively.
The aptananozymes reveal enhanced catalytic activities as compared
to the separated catalyst and respective aptamer constituents. The
catalytic functions of the aptananozymes are controlled by the structure
of the aptamer units linked to the Cu2+ ion-functionalized
C-dots. In addition, the aptananozyme shows chiroselective catalytic
functions demonstrated by the chiroselective-catalyzed oxidation of l/d-DOPA to l/d-dopachrome. Binding
studies of the substrates to the different aptananozymes and mechanistic
studies associated with the catalytic transformations are discussed.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yonatan Biniuri
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Fadeev
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Pu Zhang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Raanan Carmieli
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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24
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Tivon Y, Falcone G, Deiters A. Protein Labeling and Crosslinking by Covalent Aptamers. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yaniv Tivon
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Gianna Falcone
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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25
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Tivon Y, Falcone G, Deiters A. Protein Labeling and Crosslinking by Covalent Aptamers. Angew Chem Int Ed Engl 2021; 60:15899-15904. [PMID: 33928724 PMCID: PMC8260448 DOI: 10.1002/anie.202101174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
We developed a new approach to selectively modify native proteins in their biological environment using electrophilic covalent aptamers. These aptamers are generated through introduction of a proximity-driven electrophile at specific nucleotide sites. Using thrombin as a proof-of-concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease-resistant enzyme inhibition.
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Affiliation(s)
- Yaniv Tivon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Gianna Falcone
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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26
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Song M, Khan IM, Wang Z. Research Progress of Optical Aptasensors Based on AuNPs in Food Safety. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02029-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Zhao J, Lu Z, Wang S, Wei Z, Zhou J, Ren S, Lou X. Nanoscale Affinity Double Layer Overcomes the Poor Antimatrix Interference Capability of Aptamers. Anal Chem 2021; 93:4317-4325. [PMID: 33620193 DOI: 10.1021/acs.analchem.0c05320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Poor antimatrix interference capability of aptamers is one of the major obstacles preventing their wide applications for real-sample detections. Here, we devise a multiple-function interface, denoted as a nanoscale affinity double layer (NADL), to overcome this bottleneck via in situ simultaneous target enrichment, purification, and detection. The NADL consists of an upper aptamer layer for target purification and sensing and a lower nanoscale solid-phase microextraction (SPME) layer for sample enrichment. The targets flowing through the NADL-functionalized surface are instantly million-fold enriched and purified by the sequential extraction of aptamer and SPME. The formation of the aptamer-target complex is greatly enhanced, enabling ultrasensitive detection of targets with minimized interference from the matrix. Taking the fiber-optic evanescent wave sensor as an example, we demonstrated the feasibility and generality of the NADL. The unprecedented detection of limits of 800, 4.8, 40, and 0.14 fM were, respectively, achieved for three representative small-molecule targets with distinct hydrophobicity (kanamycin A, sulfadimethoxine, and di-(2-ethylhexyl) phthalate) and protein target (human serum albumin), corresponding to 2500 to 3 × 108-fold improvement compared to the sensors without the NADL. Our sensors also showed exceptionally high target specificity (>1000) and tunable dynamic ranges simply by manipulating the SPME layer. With these features comes the ability to directly detect targets in diluted environmental, food, and biological samples at concentrations all well below the tolerance limits.
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Affiliation(s)
- Jiaxing Zhao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Zhangwei Lu
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Shuo Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Zhenzhe Wei
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Jianshuo Zhou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Shang Ren
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
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Vázquez-González M, Willner I. Aptamer-Functionalized Micro- and Nanocarriers for Controlled Release. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9520-9541. [PMID: 33395247 DOI: 10.1021/acsami.0c17121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sequence-specific nucleic acids recognizing low-molecular-weight ligands or macromolecules (aptamers) have found growing interest for biomedical applications. The present review article summarizes recent applications of aptamers as stimuli-responsive gating units of drug (or dye)-loaded nano- or microcarriers for controlled and targeted drug release. In the presence of cellular biomarkers, the nano-/microcarriers are unlocked by forming aptamer-ligand complexes. Different aptamer-functinalized nano-/microcarriers are presented, including inorganic nanomaterials, metal-organic framework nanoparticles, and soft materials. The chemistries associated with the preparation of the carriers and the mechanisms to unlock the carriers are discussed. Stimuli-responsive gated drug-loaded micro-/nanocarriers hold great promise as functional sense-and-treat materials for the targeted and selective release of drugs.
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Affiliation(s)
- Margarita Vázquez-González
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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29
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Zahra QUA, Khan QA, Luo Z. Advances in Optical Aptasensors for Early Detection and Diagnosis of Various Cancer Types. Front Oncol 2021; 11:632165. [PMID: 33718215 PMCID: PMC7946820 DOI: 10.3389/fonc.2021.632165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer is a life-threatening concern worldwide. Sensitive and early-stage diagnostics of different cancer types can make it possible for patients to get through the best available treatment options to combat this menace. Among several new detection methods, aptamer-based biosensors (aptasensors) have recently shown promising results in terms of sensitivity, identification, or detection of either cancerous cells or the associated biomarkers. In this mini-review, we have summarized the most recent (2016-2020) developments in different approaches belonging to optical aptasensor technologies being widely employed for their simple operation, sensitivity, and early cancer diagnostics. Finally, we shed some light on limitations, advantages, and current challenges of aptasensors in clinical diagnostics, and we elaborated on some future perspectives.
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Affiliation(s)
- Qurat ul ain Zahra
- Core Facility Center for Life Sciences, Department of Biochemistry and Molecular Biology, School of Life Sciences, University of Sciences and Technology of China, Hefei, China
- Hefei National Lab for Physical Sciences at the Microscale and the Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, China
| | - Qaiser Ali Khan
- Institute of Chemistry of New Materials, Universität Osnabrück, Osnabrück, Germany
| | - Zhaofeng Luo
- Core Facility Center for Life Sciences, Department of Biochemistry and Molecular Biology, School of Life Sciences, University of Sciences and Technology of China, Hefei, China
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30
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Vázquez-González M, Willner I. Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications. Int J Mol Sci 2021; 22:1803. [PMID: 33670386 PMCID: PMC7918352 DOI: 10.3390/ijms22041803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 01/05/2023] Open
Abstract
Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.
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Affiliation(s)
- Margarita Vázquez-González
- Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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31
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Wang H, Zhang Z, Chen C, Liang A, Jiang Z. Fullerene carbon dot catalytic amplification-aptamer assay platform for ultratrace As +3 utilizing SERS/RRS/Abs trifunctional Au nanoprobes. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123633. [PMID: 32827860 DOI: 10.1016/j.jhazmat.2020.123633] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/05/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Under microwave conditions, Au-doped carbon dots (CDAu) were prepared using fullerene as a precursor, and characterized in details. It is found that CDAu can strongly catalyze the reaction of HAuCl4-fructose to generate gold nanoparticles (AuNPs). The new nanocatalytic reaction was studied by surface-enhanced Raman scattering (SERS), resonance Rayleigh scattering (RRS) and absorption (Abs) spectrometry. Based on the specific aptamer (AptAs)-As+3 reaction mediated the CDAu-HAuCl4-fructose nanoreaction, and the products of AuNPs as SERS/RRS/Abs trifunctional indicator nanoprobes, a new trimode Apt assay strategy was developed for detection of ultratrace As+3. A 0.07-0.70, 0.10-0.60 and 0.20-0.70 μg L-1 were determined by SERS, RRS and Abs, with detection limits (DL) of 0.04, 0.06, 0.10 μg L-1 respectively. The aptamer-regulation CDAu catalytic amplification platform can be also used to assay 1.7-13.3 nmol L-1 Pb2+ and 2.0-12 μmol L-1 Hg2+, with DL of 0.80 nmol L-1 and 0.90 μmol L-1 respectively.
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Affiliation(s)
- Haolin Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin 541004, China
| | - Zhihao Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin 541004, China
| | - Chunqiang Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin 541004, China
| | - Aihui Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin 541004, China.
| | - Zhiliang Jiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin 541004, China.
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32
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Paul A, Warszawik EM, Loznik M, Boersma AJ, Herrmann A. Modular and Versatile Trans‐Encoded Genetic Switches. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Avishek Paul
- Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Eliza M. Warszawik
- Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Mark Loznik
- Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Arnold J. Boersma
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- Institute of Technical and Macromolecular Chemistry RWTH Aachen University Worringerweg 2 52074 Aachen Germany
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- Institute of Technical and Macromolecular Chemistry RWTH Aachen University Worringerweg 2 52074 Aachen Germany
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33
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Paul A, Warszawik EM, Loznik M, Boersma AJ, Herrmann A. Modular and Versatile Trans-Encoded Genetic Switches. Angew Chem Int Ed Engl 2020; 59:20328-20332. [PMID: 32352201 PMCID: PMC7689881 DOI: 10.1002/anie.202001372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/10/2020] [Indexed: 01/14/2023]
Abstract
Current bacterial RNA switches suffer from lack of versatile inputs and are difficult to engineer. We present versatile and modular RNA switches that are trans-encoded and based on tRNA-mimicking structures (TMSs). These switches provide a high degree of freedom for reengineering and can thus be designed to accept a wide range of inputs, including RNA, small molecules, and proteins. This powerful approach enables control of the translation of protein expression from plasmid and genome DNA.
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Affiliation(s)
- Avishek Paul
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Eliza M. Warszawik
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Mark Loznik
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Arnold J. Boersma
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
| | - Andreas Herrmann
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- DWI-Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
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34
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Simmons MD, Miller LM, Sundström MO, Johnson S. Aptamer-Based Detection of Ampicillin in Urine Samples. Antibiotics (Basel) 2020; 9:E655. [PMID: 33003560 PMCID: PMC7601551 DOI: 10.3390/antibiotics9100655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The misuse of antibiotics in health care has led to increasing levels of drug resistant infections (DRI's) occurring in the general population. Most technologies developed for the detection of DRI's typically focus on phenotyping or genotyping bacterial resistance rather than on the underlying cause and spread of DRI's; namely the misuse of antibiotics. An aptameric based assay has been developed for the monitoring of ampicillin in urine samples, for use in determining optimal antibiotic dosage and monitoring patient compliance with treatment. The fluorescently labelled aptamers were shown to perform optimally at pH 7, ideal for buffered clinical urine samples, with limits of detection as low as 20.6 nM, allowing for determination of ampicillin in urine in the clinically relevant range of concentrations (100 nM to 100 µM). As the assay requires incubation for only 1 h with a small sample volume, 50 to 150 µL, the test would fit within current healthcare pathways, simplifying the adoption of the technology.
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Affiliation(s)
- Matthew D. Simmons
- Department of Electronic Engineering, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
| | - Lisa M. Miller
- Department of Chemistry, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
| | - Malin O. Sundström
- Department of Electronic Engineering, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
| | - Steven Johnson
- Department of Electronic Engineering, University of York, Heslington, York, North Yorkshire YO10 5DD, UK;
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35
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Mao K, Zhang H, Pan Y, Zhang K, Cao H, Li X, Yang Z. Nanomaterial-based aptamer sensors for analysis of illicit drugs and evaluation of drugs consumption for wastewater-based epidemiology. Trends Analyt Chem 2020; 130:115975. [PMID: 32834242 PMCID: PMC7336936 DOI: 10.1016/j.trac.2020.115975] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The abuse of illicit drugs usually associated with dramatic crimes may cause significant problems for the whole society. Wastewater-based epidemiology (WBE) has been demonstrated to be a novel and cost-effective way to evaluate the abuse of illicit drugs at the community level, and has been used as a routine method for monitoring and played a significant role for combating the crimes in some countries, e.g. China. The method can also provide temporal and spatial variation of drugs of abuse. The detection methods mainly remain on the conventional liquid chromatography coupled with mass spectrometry, which is extremely sensitive and selective, however needs advanced facility and well-trained personals, thus limit it in the lab. As an alternative, sensors have emerged to be a powerful analytical tool for a wide spectrum of analytes, in particular aptamer sensors (aptasensors) have attracted increasing attention and could act as an efficient tool in this field due to the excellent characteristics of selectivity, sensitivity, low cost, miniaturization, easy-to-use, and automation. In this review, we will briefly introduce the context, specific assessment process and applications of WBE and the recent progress of illicit drug aptasensors, in particular focusing on optical and electrochemical sensors. We then highlight several recent aptasensors for illicit drugs in new technology integration and discuss the feasibility of these aptasensor for WBE. We will summarize the challenges and propose our insights and opportunity on aptasensor for WBE to evaluate community-wide drug use trends and public health.
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Affiliation(s)
- Kang Mao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Yuwei Pan
- Cranfield Water Science Institute, Cranfield University, Cranfield, MK43 0AL, United Kingdom
| | - Kuankuan Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Haorui Cao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Xiqing Li
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Zhugen Yang
- Cranfield Water Science Institute, Cranfield University, Cranfield, MK43 0AL, United Kingdom
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Prante M, Segal E, Scheper T, Bahnemann J, Walter J. Aptasensors for Point-of-Care Detection of Small Molecules. BIOSENSORS 2020; 10:E108. [PMID: 32859075 PMCID: PMC7559136 DOI: 10.3390/bios10090108] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Aptamers, a group of nucleic acids which can specifically bind to a target molecule, have drawn extensive interest over the past few decades. For analytics, aptamers represent a viable alternative to gold-standard antibodies due to their oligonucleic nature combined with advantageous properties, including higher stability in harsh environments and longer shelf-life. Indeed, over the last decade, aptamers have been used in numerous bioanalytical assays and in various point-of-care testing (POCT) platforms. The latter allows for rapid on-site testing and can be performed outside a laboratory by unskilled labor. Aptamer technology for POCT is not limited just to medical diagnostics; it can be used for a range of applications, including environmental monitoring and quality control. In this review, we critically examine the use of aptamers in POCT with an emphasis on their advantages and limitations. We also examine the recent success of aptasensor technology and how these findings pave the way for the analysis of small molecules in POCT and other health-related applications. Finally, the current major limitations of aptamers are discussed, and possible approaches for overcoming these challenges are presented.
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Affiliation(s)
- Marc Prante
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Technion City, Haifa 3200003, Israel;
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
| | - Janina Bahnemann
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
| | - Johanna Walter
- Institute of Technical Chemistry, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany; (M.P.); (T.S.); (J.B.)
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37
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Zhou Z, Sohn YS, Nechushtai R, Willner I. DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer-Ligand Complexes. ACS NANO 2020; 14:9021-9031. [PMID: 32539340 PMCID: PMC7467810 DOI: 10.1021/acsnano.0c04031] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/15/2020] [Indexed: 05/21/2023]
Abstract
The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore-quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, EcoRI, and HindIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore-quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer-ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.
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Affiliation(s)
- Zhixin Zhou
- Institute
of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute
of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute
of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- E-mail:
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38
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Hornung T, O’Neill HA, Logie SC, Fowler KM, Duncan JE, Rosenow M, Bondre AS, Tinder T, Maher V, Zarkovic J, Zhong Z, Richards MN, Wei X, Miglarese MR, Mayer G, Famulok M, Spetzler D. ADAPT identifies an ESCRT complex composition that discriminates VCaP from LNCaP prostate cancer cell exosomes. Nucleic Acids Res 2020; 48:4013-4027. [PMID: 31989173 PMCID: PMC7192620 DOI: 10.1093/nar/gkaa034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/03/2020] [Accepted: 01/15/2020] [Indexed: 12/15/2022] Open
Abstract
Libraries of single-stranded oligodeoxynucleotides (ssODNs) can be enriched for sequences that specifically bind molecules on naïve complex biological samples like cells or tissues. Depending on the enrichment strategy, the ssODNs can identify molecules specifically associated with a defined biological condition, for example a pathological phenotype, and thus are potentially useful for biomarker discovery. We performed ADAPT, a variant of SELEX, on exosomes secreted by VCaP prostate cancer cells. A library of ∼1011 ssODNs was enriched for those that bind to VCaP exosomes and discriminate them from exosomes derived from LNCaP prostate cancer cells. Next-generation sequencing (NGS) identified the best discriminating ssODNs, nine of which were resynthesized and their discriminatory ability confirmed by qPCR. Affinity purification with one of the sequences (Sequence 7) combined with LC–MS/MS identified its molecular target complex, whereof most proteins are part of or associated with the multiprotein ESCRT complex participating in exosome biogenesis. Within this complex, YBX1 was identified as the directly-bound target protein. ADAPT thus is able to differentiate exosomes from cancer cell subtypes from the same lineage. The composition of ESCRT complexes in exosomes from VCaP versus LNCaP cells might constitute a discriminatory element between these prostate cancer subtypes.
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Affiliation(s)
- Tassilo Hornung
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | | | - Stephen C Logie
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | | | - Janet E Duncan
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Matthew Rosenow
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Aniket S Bondre
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Teresa Tinder
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Varun Maher
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Jelena Zarkovic
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Zenyu Zhong
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | | | - Xixi Wei
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
| | - Mark R Miglarese
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
- Correspondence may also be addressed to Mark R. Miglarese.
| | - Günter Mayer
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Correspondence may also be addressed to Günter Mayer.
| | - Michael Famulok
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Max-Planck-Fellow Chemical Biology, Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
- To whom correspondence should be addressed. Tel: +49 228 731787; Fax: +49 228 735388;
| | - David Spetzler
- Caris Life Sciences, 4610 South 44th Place, Phoenix, AZ 85040, USA
- Correspondence may also be addressed to David Spetzler. Tel: +1 602 464 7527;
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39
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Vázquez-González M, Willner I. Stimuli-Responsive Biomolecule-Based Hydrogels and Their Applications. Angew Chem Int Ed Engl 2020; 59:15342-15377. [PMID: 31730715 DOI: 10.1002/anie.201907670] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/10/2019] [Indexed: 12/16/2022]
Abstract
This Review presents polysaccharides, oligosaccharides, nucleic acids, peptides, and proteins as functional stimuli-responsive polymer scaffolds that yield hydrogels with controlled stiffness. Different physical or chemical triggers can be used to structurally reconfigure the crosslinking units and control the stiffness of the hydrogels. The integration of stimuli-responsive supramolecular complexes and stimuli-responsive biomolecular units as crosslinkers leads to hybrid hydrogels undergoing reversible triggered transitions across different stiffness states. Different applications of stimuli-responsive biomolecule-based hydrogels are discussed. The assembly of stimuli-responsive biomolecule-based hydrogel films on surfaces and their applications are discussed. The coating of drug-loaded nanoparticles with stimuli-responsive hydrogels for controlled drug release is also presented.
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Affiliation(s)
| | - Itamar Willner
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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40
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Vázquez‐González M, Willner I. Stimuliresponsive, auf Biomolekülen basierende Hydrogele und ihre Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201907670] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Itamar Willner
- Institute of Chemistry Hebrew University of Jerusalem Jerusalem 91904 Israel
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41
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Wang X, Cheng Y, Cai S, Chen J, Xu P, Chen Y, Yu H, Xu T, Zhang S, Li X. Resonant-Cantilever-Detected Kinetic/Thermodynamic Parameters for Aptamer-Ligand Binding on a Liquid-Solid Interface. Anal Chem 2020; 92:11127-11134. [PMID: 32551574 DOI: 10.1021/acs.analchem.0c01142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acid aptamers have been widely used as recognition elements on various biosensing interfaces, but quantitative kinetic/thermodynamic analysis for revealing the aptamer-ligand binding mechanism, which occurs on a liquid-solid interface, has not been realized due to a lack of usable biophysical tools. Herein we apply a resonant microcantilever sensor to continuously record the frequency shift according to the binding-induced mass change on the liquid-solid interface. The frequency-shift curve is used for tracing the reaction process and is fitted with classic equations to calculate a set of kinetic/thermodynamic parameters, such as rate constants (ka = 902.95 M-1 s-1, kd = 0.000141 s-1), equilibrium constants (KD = 1.55 μM), the Gibbs free energy (ΔG° = -32.57 kJ/mol), and the activation energy (Ea = 38.03 kJ/mol) for the immobilized aptamer and free ATP. This quantitative analysis method is label-free, calibration-free, and highly sensitive. The kinetic/thermodynamic parameter detection method provides new resolution to the in-depth understanding of the ligand-aptamer interaction on the liquid-solid interface for biosensing or lab-on-a-chip applications.
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Affiliation(s)
- Xuefeng Wang
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yarong Cheng
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Shengran Cai
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianzhong Chen
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Xu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Chen
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haitao Yu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiegang Xu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Zhang
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Xinxin Li
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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42
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Luo G, Biniuri Y, Chen W, Wang J, Neumann E, Marjault H, Nechushtai R, Winkler M, Happe T, Willner I. Modelling Photosynthesis with Zn
II
‐Protoporphyrin All‐DNA G‐Quadruplex/Aptamer Scaffolds. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Guo‐Feng Luo
- Institute of Chemistry and Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Yonatan Biniuri
- Institute of Chemistry and Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Wei‐Hai Chen
- Institute of Chemistry and Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- Institute of Chemistry and Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Ehud Neumann
- Institute of Life Science The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | | | - Rachel Nechushtai
- Institute of Life Science The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Martin Winkler
- Department of Biochemistry of Plants Ruhr-University Bochum Germany
| | - Thomas Happe
- Department of Biochemistry of Plants Ruhr-University Bochum Germany
| | - Itamar Willner
- Institute of Chemistry and Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
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43
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Luo GF, Biniuri Y, Chen WH, Wang J, Neumann E, Marjault HB, Nechushtai R, Winkler M, Happe T, Willner I. Modelling Photosynthesis with Zn II -Protoporphyrin All-DNA G-Quadruplex/Aptamer Scaffolds. Angew Chem Int Ed Engl 2020; 59:9163-9170. [PMID: 32125762 DOI: 10.1002/anie.202002915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Indexed: 01/03/2023]
Abstract
All-DNA scaffolds act as templates for the organization of photosystem I model systems. A series of DNA templates composed of ZnII -protoporphyrin IX (ZnII PPIX)-functionalized G-quadruplex conjugated to the 3'- or 5'-end of the tyrosinamide (TA) aptamer and ZnII PPIX/G-quadruplex linked to the 3'- and 5'-ends of the TA aptamer through a four-thymidine bridge. Effective photoinduced electron transfer (ET) from ZnII PPIX/G-quadruplex to bipyridinium-functionalized tyrosinamide, TA-MV2+ , bound to the TA aptamer units is demonstrated. The effectiveness of the primary ET quenching of ZnII PPIX/G-quadruplex by TA-MV2+ controls the efficiency of the generation of TA-MV+. . The photosystem-controlled formation of TA-MV+. by the different photosystems dictates the secondary activation of the ET cascade corresponding to the ferredoxin-NADP+ reductase (FNR)-catalysed reduction of NADP+ to NADPH by TA-MV+. , and the sequestered alcohol dehydrogenase catalysed reduction of acetophenone to 1-phenylethanol by NADPH.
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Affiliation(s)
- Guo-Feng Luo
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yonatan Biniuri
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Wei-Hai Chen
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Jianbang Wang
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ehud Neumann
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | | | - Rachel Nechushtai
- Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Martin Winkler
- Department of Biochemistry of Plants, Ruhr-University Bochum, Germany
| | - Thomas Happe
- Department of Biochemistry of Plants, Ruhr-University Bochum, Germany
| | - Itamar Willner
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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44
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Zhang P, Yue L, Vázquez-González M, Zhou Z, Chen WH, Sohn YS, Nechushtai R, Willner I. MicroRNA-Guided Selective Release of Loads from Micro-/Nanocarriers Using Auxiliary Constitutional Dynamic Networks. ACS NANO 2020; 14:1482-1491. [PMID: 31927975 PMCID: PMC7467758 DOI: 10.1021/acsnano.9b06047] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/13/2020] [Indexed: 05/20/2023]
Abstract
Two different drug micro-carriers consisting of doxorubicin-dextran (DOX-D)- and camptothecin-modified carboxymethyl cellulose (CPT-CMC)-loaded nucleic acid-stabilized microcapsules, MC-1 and MC-2, or two different nanocarriers consisting of nucleic-acid-locked doxorubicin (DOX)- and camptothecin (CPT)-loaded metal-organic framework nanoparticles, NMOF-1 and NMOF-2, are coupled to auxiliary constitutional dynamic networks, CDNs, for the triggered release of the drugs. CDN "S" composed of four constituents AA'', AB', BA', and BB', and two hairpin structures, H1 and H2, leads to the CDN "S"-guided unlocking of the MC-1/MC-2 carriers and the release of DOX-D and CPT-CMC or of the NMOF-1 and NMOF-2 carriers that release DOX and CPT, respectively. The unlocking processes are activated by the cleavage of H1 and H2 by BB' and BA', respectively, to yield fragmented strands that unlock the gating units of the microcapsules/NMOFs carriers. In the presence of miRNA-155 or miRNA-124, dictated orthogonal reconfiguration of CDN "S" into CDN "X" or "Y" proceeds. The miRNA-155 stimulates the reconfiguration of CDN "S" to CDN "X", where AA' and BB' are upregulated, and AB' and BA' are downregulated, leading to the enhanced release of DOX-D or DOX from the microcapsule/NMOFs carriers, and to the concomitant inhibition of the release of CPT-CMC or CPT from the respective carriers. Similarly, the miRNA-124-triggered reconfiguration of CDN "S" to CDN "Y" results in the BA'-guided cleavage of H2 and the preferred release of CPT-CMC or CPT from the respective carriers. The miRNA-triggered CDN-driven unlocking of the carriers stimulates the amplified and selective release of the drugs from the microcapsules/NMOFs carriers.
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Affiliation(s)
- Pu Zhang
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liang Yue
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Margarita Vázquez-González
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Wei-Hai Chen
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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45
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Biniuri Y, Luo GF, Fadeev M, Wulf V, Willner I. Redox-Switchable Binding Properties of the ATP-Aptamer. J Am Chem Soc 2019; 141:15567-15576. [PMID: 31478647 DOI: 10.1021/jacs.9b06256] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this study, we report on a redox-controllable and reversible complete "ON"/"OFF"-switchable aptamer binding to ATP. A series of methylene blue-modified ATP-aptamers was synthesized, revealing improved binding affinities toward ATP as compared to the nonmodified aptamer. These binding affinities were dependent on the conjugation site of the redox label on the aptamer scaffold. Importantly, we find that the oxidized methylene blue-modified aptamers bind to ATP with micromolar affinity, while the reduced form lacks binding affinity toward ATP, resulting in an unprecedented complete "ON"/"OFF" redox-controllable aptamer switch. We demonstrate the cyclic "ON"/"OFF" binding of ATP to the methylene blue-functionalized aptamer through cyclic oxidation and reduction of the redox label using both chemical and electrochemical means. Molecular dynamics and docking simulations were performed to account for the redox-switchable properties of the conjugated aptamers and to rationalize the enhanced binding affinities of the different aptamer designs.
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Affiliation(s)
- Yonatan Biniuri
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Guo-Feng Luo
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Michael Fadeev
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Verena Wulf
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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46
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Luo GF, Biniuri Y, Chen WH, Neumann E, Fadeev M, Marjault HB, Bedi A, Gidron O, Nechushtai R, Stone D, Happe T, Willner I. Artificial Photosynthesis with Electron Acceptor/Photosensitizer-Aptamer Conjugates. NANO LETTERS 2019; 19:6621-6628. [PMID: 31407917 DOI: 10.1021/acs.nanolett.9b02880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sequence-specific aptamers act as functional scaffolds for the assembly of photosynthetic model systems. The Ru(II)-tris-bipyridine photosensitizer is conjugated by different binding modes to the antityrosinamide aptamer to yield a set of photosensitizer-aptamer binding scaffolds. The N-methyl-N'-(3-aminopropane)-4,4'-bipyridinium electron acceptor, MV2+, is covalently linked to tyrosinamide, TA, to yield the conjugate TA-MV2+. The tyrosinamide unit in TA-MV2+ acts as a ligand for anchoring TA-MV2+ to the Ru(II)-tris-bipyridine-aptamer scaffold, generating the diversity of photosensitizer-aptamer/electron acceptor supramolecular conjugates. Effective electron transfer quenching in the photosynthetic model systems is demonstrated, and the quenching efficiencies are controlled by the structural features of the conjugates. The redox species generated by the photosensitizer-aptamer/electron acceptor supramolecular systems mediate the ferredoxin-NADP+ reductase, FNR, catalyzed synthesis of NADPH, and the Pt-nanoparticle-catalyzed evolution of hydrogen (H2). The novelty of the study rests on the unprecedented use of aptamer scaffolds as functional units for organizing photosynthetic model systems.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Thomas Happe
- Fakultät für Biologie und Biotechnologie, AG Photobiotechnologie , Ruhr Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany
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Abstract
Antibodies are large proteins generated in vivo to bind specifically to a wide spectrum of targets ranging from biological to environmental molecules. They play a vital role in research, diagnostics, sensing, and therapeutic applications. Over the past few decades, advancements have been made to improve the performance of antibodies, specifically in the area of immunosensors. However, there has been an urgent need for alternative high-quality recognition probes that can be produced synthetically in bulk quantity to ensure better reproducibility and lower cost, as well as avoiding the need of using animals in the production process. Aptamers are synthetic nucleic acid single-stranded (ss) DNAs or RNAs that can bind with high affinity and specificity to their targets. They can be generated via in vitro section protocol, known as systematic evolution of ligands by exponential enrichment (SELEX). The advantages of aptamers promoted their successful incorporation in several signal transduction schemes, some of which reached the commercial market for point-of-care and in-field applications. This chapter describes the two types of affinity reagents: antibodies and aptamers, and their methods of production, advantages, and limitations. The focus will be directed at their incorporation in analytical transduction methods and how aptamer molecular size as well as unique conformational change upon target binding has triggered the evolution of new sensing methods.
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Affiliation(s)
- Omar A. Alsager
- National Center for Irradiation Technology, Nuclear Science Research Institute, King Abdulaziz City for Science and Technology P.O. Box 6086 Riyadh 11442 Saudi Arabia
| | - Shimaa Eissa
- Department of Chemistry, Alfaisal University Al Zahrawi Street, Al Maather, Al Takhassusi Rd Riyadh 11533 Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University Al Zahrawi Street, Al Maather, Al Takhassusi Rd Riyadh 11533 Saudi Arabia
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Wu YY, Huang P, Wu FY. A label-free colorimetric aptasensor based on controllable aggregation of AuNPs for the detection of multiplex antibiotics. Food Chem 2019; 304:125377. [PMID: 31476547 DOI: 10.1016/j.foodchem.2019.125377] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/12/2019] [Accepted: 08/17/2019] [Indexed: 11/26/2022]
Abstract
We devise a novel colorimetric aptasensor for multiplex antibiotics based on an ss-DNA fragment coordinately controlling gold nanoparticles (AuNPs) aggregation. The multifunctional aptamer (Apt) was elaborately designed to be adsorbed on AuNPs surfaces acting as a binding element for antibiotics and a molecular switch. Chloramphenicol (CAP) and tetracycline (TET) were selected as the model antibiotics. When one kind of antibiotics was added, the specifically recognized fragment of Apt can bind to it and dissociated, and the non-specific one coordinately controls AuNPs aggregation under high-salt conditions. Hence, different color changes of AuNPs solution can be used as the signal readout. The aptasensor exhibited remarkable selectivity and sensitivity for separate detection of TET and CAP, and the detection limits are estimated to be 32.9 and 7.0 nM, respectively. The analysis with the absorption spectroscopy and the smartphone are applied to detect antibiotics in real samples with consistent results and desirable recoveries.
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Affiliation(s)
- Yang-Yang Wu
- College of Chemistry, Nanchang University, Nanchang 330031, China
| | - Pengcheng Huang
- College of Chemistry, Nanchang University, Nanchang 330031, China
| | - Fang-Ying Wu
- College of Chemistry, Nanchang University, Nanchang 330031, China.
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Gao S, Hu W, Zheng X, Cai S, Wu J. Functionalized aptamer with an antiparallel G-quadruplex: Structural remodeling, recognition mechanism, and diagnostic applications targeting CTGF. Biosens Bioelectron 2019; 142:111475. [PMID: 31288216 DOI: 10.1016/j.bios.2019.111475] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/01/2019] [Accepted: 06/24/2019] [Indexed: 01/01/2023]
Abstract
Connective tissue growth factor (CTGF), a widely used biomarker, is involved in many diseases, such as diabetic retinopathy, diabetic nephropathy, and rheumatoid arthritis, and it is often over-expressed in human malignant tumors. Therefore, sensitive, specific and efficient detection methods for CTGF are needed for the early diagnosis and assessment of prognosis. In this study, an aptamer, APT1, that specifically binds to CTGF was obtained by SELEX technology. Circular dichroism spectroscopy indicated that APT1 formed interconvertible parallel and antiparallel G-quadruplexes. Mutation and truncation strategies optimized APT1 and improved its functions, yielding APT1M6T, which folded into an antiparallel G-quadruplex with higher targeting affinity. A stable APT1M6T-CTGF complex model was established by molecular simulation, which helped elucidate the molecular recognition mechanism of APT1M6T and CTGF and also provided experimental guidance for rational site-directed modification of APT1M6T. A locked nucleic acid sequence was then integrated into APT1M6T to generate APT1M6TL, which had higher structural stability. A BLI-based enzyme-linked aptamer sandwich assay (BLI-ELASA) was successfully developed. The method exhibited a broad detection range from 0.05 to 50 nM with a low detection limit of 0.02 nM. The method showed high selectivity, reproducibility, and stability for analysis of CTGF in spiked serum and urine samples. This developed BLI-ELASA is promising and enables real-time, sensitive and rapid detection of the disease-specific biomarker CTGF.
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Affiliation(s)
- Shunxiang Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China; Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Wei Hu
- Chengdu FenDi Technology Co., Ltd., Chengdu, China
| | - Xin Zheng
- Department of Clinical Laboratory, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, China.
| | - Jihong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China; Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China.
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50
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Sensor for ampicillin based on a microwave electrodynamic resonator. Biosens Bioelectron 2019; 130:95-102. [DOI: 10.1016/j.bios.2019.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/07/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
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