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Park SV, Kang B, Lee M, Yoo H, Jo H, Woo S, Oh SS. In vitro selection of a trans aptamer complex for target-responsive fluorescence activation. Anal Chim Acta 2024; 1301:342465. [PMID: 38553123 DOI: 10.1016/j.aca.2024.342465] [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: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions. RESULTS By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges. SIGNIFICANCE This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.
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Affiliation(s)
- Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Minjong Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sungwook Woo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
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2
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Du M, Cheng X, Chen Q, Xu X. A novel and sensitive electrochemical aptasensor for sulfadimethoxine detection based on the triple helix/exonuclease I-assisted double-amplification strategy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1570-1578. [PMID: 38407003 DOI: 10.1039/d3ay02157b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In this paper, a novel and sensitive electrochemical aptasensor for sulfadimethoxine (SDM) detection has been designed based on the triple helix structure/exonuclease I (Exo I)-assisted double signal amplification strategy. The aptamer probe (Apt) hybridizes with the signal transduction probe (STP) on the electrode to form a rigid double-stranded DNA (dsDNA) structure, so that the STP remains upright and methylene blue (MB) on the STP is far away from the electrode surface, resulting in a delicate current signal. In the presence of SDM, the SDM and Apt combine into a complex, leading to the transfer of the Apt and the exposure of the STP. Meanwhile, the added Exo I can digest the Apt to realize the cyclic amplification of SDM. After the addition of the signal probe (SP), a triple helix structure between the SP and STP is formed under acidic conditions, and MB on the STP and SP collide with the electrode surface to generate a strong electrochemical signal. The proposed aptasensor combines the features of the triple helix structure and Exo I to achieve double signal amplification for the sensitive detection of SDM with a wide linear range of 0.05-1000 ng mL-1 and a low detection limit of 0.02 ng mL-1. Furthermore, it has been successfully used to detect SDM in milk and lake water samples.
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Affiliation(s)
- Meijuan Du
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China.
| | - Xin Cheng
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China.
| | - Qian Chen
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China.
| | - Xueqin Xu
- Key Laboratory for Analytical Science of Food Safety and Biology, MOE, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China.
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3
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Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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4
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Wang L, Yao L, Ma Q, Mao Y, Qu H, Zheng L. Investigation on small molecule-aptamer dissociation equilibria based on antisense displacement probe. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Nejabat M, Samie A, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. An Overview on Gold Nanorods as Versatile Nanoparticles in Cancer Therapy. J Control Release 2023; 354:221-242. [PMID: 36621644 DOI: 10.1016/j.jconrel.2023.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/10/2023]
Abstract
Gold nanorods (GNRs/AuNRs) are a group of gold nanoparticles which their simple surface chemistry allows for various surface modifications, providing the possibility of using them in the fabrication of biocompatible and functional nano-agents for cancer therapy. AuNRs, moreover, exhibit a maximum absorption of longitudinal localized surface plasmon resonance (LSPR) in the near-infrared (NIR) region which overlaps with NIR bio-tissue 'window' suggesting that they are proper tools for thermal ablation of cancer cells. AuNRs can be used for induction of mono or combination therapies by administering various therapeutic approaches such as photothermal therapy (PTT), photodynamic therapy (PDT), chemotherapy (CT), radiotherapy (RT), and gene therapy (GT). In this review, anticancer therapeutic capacities of AuNRs along with different surface modifications are summarized comprehensively. The roles of AuNRs in fabrication of various nano-constructs are also discussed.
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Affiliation(s)
- Masoud Nejabat
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Samie
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Huang Y, Nguyen MK, Nguyen VH, Loo J, Lehtonen AJ, Kuzyk A. Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2954-2960. [PMID: 35212547 PMCID: PMC8908738 DOI: 10.1021/acs.langmuir.1c03434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Aptamers have emerged as versatile affinity ligands and as promising alternatives to protein antibodies. However, the inconsistency in the reported affinities and specificities of aptamers has greatly hindered the development of aptamer-based applications. Herein, we present a strategy to characterize aptamers by using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. We demonstrate the characterization of several DNA aptamers, including aptamers for small molecules and macromolecules, as well as aptamers with high and low affinities. The presented characterization scheme can be readily adapted to a wide selection of aptamers. We anticipate that our approach will advance the development of aptamer-based applications by enabling reliable and reproducible characterization of aptamers.
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Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dist. 10, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University Ho Chi Minh City,
Linh Trung Ward, Thu Duc District, 700000 Ho Chi Minh City, Vietnam
| | - Vu Hoang Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Arttu J. Lehtonen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Department
of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
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Billet B, Chovelon B, Fiore E, Faure P, Ravelet C, Peyrin E. Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions. Biosens Bioelectron 2022; 205:114091. [PMID: 35217256 DOI: 10.1016/j.bios.2022.114091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022]
Abstract
We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni2+ or Co2+ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.
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Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
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8
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Aptamer-modified biosensors to visualize neurotransmitter flux. J Neurosci Methods 2022; 365:109386. [PMID: 34653500 DOI: 10.1016/j.jneumeth.2021.109386] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/23/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022]
Abstract
Chemical biosensors with the capacity to continuously monitor various neurotransmitter dynamics can be powerful tools to understand complex signaling pathways in the brain. However, in vivo detection of neurochemicals is challenging for many reasons such as the rapid release and clearance of neurotransmitters in the extracellular space, or the low target analyte concentrations in a sea of interfering biomolecules. Biosensing platforms with adequate spatiotemporal resolution coupled to specific and selective receptors termed aptamers, demonstrate high potential to tackle such challenges. Herein, we review existing literature in this field. We first discuss nanoparticle-based systems, which have a simple in vitro implementation and easily interpretable results. We then examine methods employing near-infrared detection for deeper tissue imaging, hence easier translation to in vivo implementation. We conclude by reviewing live cell imaging of neurotransmitter release via aptamer-modified platforms. For each of these sensors, we discuss the associated challenges for translation to real-time in vivo neurochemical imaging. Realization of in vivo biosensors for neurotransmitters will drive future development of early prevention strategies, treatments, and therapeutics for psychiatric and neurodegenerative diseases.
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Sen RK, Prabhakar P, Bisht N, Patel M, Mishra S, Yadav AK, Venu DV, Gupta GK, Solanki PR, Ramakrishnan S, Mondal D, Srivastava AK, Dwivedi N, Dhand C. 2D Materials-Based Aptamer Biosensors: Present Status and Way Forward. Curr Med Chem 2021; 29:5815-5849. [PMID: 34961455 DOI: 10.2174/0929867328666211213115723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/13/2021] [Accepted: 10/26/2021] [Indexed: 11/22/2022]
Abstract
Current advances in constructing functional nanomaterials and elegantly designed nanostructures have opened up new possibilities for the fabrication of viable field biosensors. Two-dimensional materials (2DMs) have fascinated much attention due to their chemical, optical, physicochemical, and electronic properties. They are ultrathin nanomaterials with unique properties such as high surface-to-volume ratio, surface charge, shape, high anisotropy, and adjustable chemical functionality. 2DMs such as graphene-based 2D materials, Silicate clays, layered double hydroxides (LDHs), MXenes, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs) offer intensified physicochemical and biological functionality and have proven to be very promising candidates for biological applications and technologies. 2DMs have a multivalent structure that can easily bind to single-stranded DNA/RNA (aptamers) through covalent, non-covalent, hydrogen bond, and π-stacking interactions, whereas aptamers have a small size, excellent chemical stability, and low immunogenicity with high affinity and specificity. This review discussed the potential of various 2D material-based aptasensor for diagnostic applications, e.g., protein detection, environmental monitoring, pathogens detection, etc.
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Affiliation(s)
- Raj Kumar Sen
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Priyanka Prabhakar
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Neha Bisht
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Monika Patel
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Shruti Mishra
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Amit Kumar Yadav
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067. India
| | - Divya Vadakkumana Venu
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Gaurav Kumar Gupta
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067. India
| | - Seeram Ramakrishnan
- Center for Nanofibers and Nanotechnology, Department of Mechanical Engineering, Faculty of Engineering, 2 Engineering Drive 3, National University of Singapore, Singapore, 117576. Singapore
| | - Dehipada Mondal
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | | | - Neeraj Dwivedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Chetna Dhand
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
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Koklu A, Ohayon D, Wustoni S, Druet V, Saleh A, Inal S. Organic Bioelectronic Devices for Metabolite Sensing. Chem Rev 2021; 122:4581-4635. [PMID: 34610244 DOI: 10.1021/acs.chemrev.1c00395] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electrochemical detection of metabolites is essential for early diagnosis and continuous monitoring of a variety of health conditions. This review focuses on organic electronic material-based metabolite sensors and highlights their potential to tackle critical challenges associated with metabolite detection. We provide an overview of the distinct classes of organic electronic materials and biorecognition units used in metabolite sensors, explain the different detection strategies developed to date, and identify the advantages and drawbacks of each technology. We then benchmark state-of-the-art organic electronic metabolite sensors by categorizing them based on their application area (in vitro, body-interfaced, in vivo, and cell-interfaced). Finally, we share our perspective on using organic bioelectronic materials for metabolite sensing and address the current challenges for the devices and progress to come.
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Affiliation(s)
- Anil Koklu
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - David Ohayon
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Shofarul Wustoni
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Victor Druet
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Abdulelah Saleh
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
| | - Sahika Inal
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering (BESE), Organic Bioelectronics Laboratory, Thuwal 23955-6900, Saudi Arabia
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11
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Sanford AA, Rangel AE, Feagin TA, Lowery RG, Argueta-Gonzalez HS, Heemstra JM. RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors. Chem Sci 2021; 12:11692-11702. [PMID: 34659704 PMCID: PMC8442683 DOI: 10.1039/d1sc02715h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/23/2021] [Indexed: 11/21/2022] Open
Abstract
Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to a functional output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 μM to 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small-molecule targets.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Alexandra E Rangel
- Department of Chemistry, Center for Cell and Genome Science, University of Utah Salt Lake City Utah 84112 USA
| | - Trevor A Feagin
- Department of Chemistry, Center for Cell and Genome Science, University of Utah Salt Lake City Utah 84112 USA
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12
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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13
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Ebrahimi SB, Samanta D, Partridge BE, Kusmierz CD, Cheng HF, Grigorescu AA, Chávez JL, Mirau PA, Mirkin CA. Programming Fluorogenic DNA Probes for Rapid Detection of Steroids. Angew Chem Int Ed Engl 2021; 60:15260-15265. [PMID: 33878237 DOI: 10.1002/anie.202103440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/13/2021] [Indexed: 12/24/2022]
Abstract
The ability of aptamers to recognize a variety of different molecules has fueled their emergence as recognition agents to probe complex media and cells. Many detection strategies require aptamer binding to its target to result in a dramatic change in structure, typically from an unfolded to a folded state. Here, we report a strategy based on forced intercalation (FIT) that increases the scope of aptamer recognition by transducing subtle changes in aptamer structures into fluorescent readouts. By screening a library of green-fluorescent FIT-aptamers whose design is guided by computational modeling, we could identify hits that sense steroids like dehydroepiandrosterone sulfate (DHEAS) down to 1.3 μM with no loss in binding affinity compared to the unmodified aptamer. This enabled us to study DHEAS in clinical serum samples with several advantages over gold standard methods, including rapid readout (<30 min), simple instrumentation (plate-reader), and low sample volumes (10 μL).
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Affiliation(s)
- Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Devleena Samanta
- Department of Chemistry and International Institute for, Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Benjamin E Partridge
- Department of Chemistry and International Institute for, Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Caroline D Kusmierz
- Department of Chemistry and International Institute for, Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Ho Fung Cheng
- Department of Chemistry and International Institute for, Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Arabela A Grigorescu
- Keck Biophysics Facility, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Jorge L Chávez
- Airman Systems Directorate and 711th Human Performance Wing, Air Force Research Laboratory, 2510 Fifth St, Area B Bldg 840, WPAFB, OH, 45433, USA
| | - Peter A Mirau
- Materials and Manufacturing Directorate, Air Force Research Laboratory, 2941 Hobson Way, WPAFB, OH, 45433, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for, Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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14
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Ebrahimi SB, Samanta D, Partridge BE, Kusmierz CD, Cheng HF, Grigorescu AA, Chávez JL, Mirau PA, Mirkin CA. Programming Fluorogenic DNA Probes for Rapid Detection of Steroids. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sasha B. Ebrahimi
- Department of Chemical and Biological Engineering Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Devleena Samanta
- Department of Chemistry and International Institute for, Nanotechnology Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Benjamin E. Partridge
- Department of Chemistry and International Institute for, Nanotechnology Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Caroline D. Kusmierz
- Department of Chemistry and International Institute for, Nanotechnology Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Ho Fung Cheng
- Department of Chemistry and International Institute for, Nanotechnology Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Arabela A. Grigorescu
- Keck Biophysics Facility Northwestern University 2220 Campus Drive Evanston IL 60208 USA
| | - Jorge L. Chávez
- Airman Systems Directorate and 711th Human Performance Wing Air Force Research Laboratory 2510 Fifth St, Area B Bldg 840 WPAFB OH 45433 USA
| | - Peter A. Mirau
- Materials and Manufacturing Directorate Air Force Research Laboratory 2941 Hobson Way WPAFB OH 45433 USA
| | - Chad A. Mirkin
- Department of Chemistry and International Institute for, Nanotechnology Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
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15
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Li Y, Liu J. Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds. Analyst 2021; 145:6753-6768. [PMID: 32909556 DOI: 10.1039/d0an00886a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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16
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Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo MA, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post-Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021; 60:12346-12350. [PMID: 33742515 DOI: 10.1002/anie.202102254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Indexed: 12/11/2022]
Abstract
We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb2+ , Cd2+ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.
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Affiliation(s)
- Blandine Billet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Benoit Chovelon
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Emmanuelle Fiore
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Farid Oukacine
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | | | - Patrice Faure
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Corinne Ravelet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Eric Peyrin
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
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17
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Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo M, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post‐Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Blandine Billet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Benoit Chovelon
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Emmanuelle Fiore
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Farid Oukacine
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | | | - Patrice Faure
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Corinne Ravelet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Eric Peyrin
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
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18
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Xiong X, Dang W, Luo R, Long Y, Tong C, Yuan L, Liu B. A graphene-based fluorescent nanoprobe for simultaneous imaging of dual miRNAs in living cells. Talanta 2020; 225:121947. [PMID: 33592702 DOI: 10.1016/j.talanta.2020.121947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are regarded as important biomarkers for disease diagnostics and therapeutics due to their significant regulatory roles in physiologic and pathologic processes. Herein, a versatile nanoprobe based on reduced graphene oxide (rGO) and nucleic acid (DNA) probe was prepared for simultaneously visualize miR-451a and miR-214-3p in living cells. In vitro experiments demonstrated that the nanoprobe exhibits excellent selectivity and outstanding sensitivity as low as 1 nM towards miR-451a and miR-214-3p. Moreover, the detection signals of miRNAs have good linearity in their respective concentration ranges (miR-451a: 1-100 nM, Y1 = 9.3062X1+114.85 (R2 = 0.9965). miR-214-3p: 1-200 nM, Y2 = 1.4424X2+91.312 (R2 = 0.9961)). Finally, simultaneous dual-color imaging of miR-451a and miR-214-3p in human breast cancer cells (MDA-MB-231) was realized by exploiting the P1&P2@rGO nanoprobe. In summary, this simple and effective strategy provides a general sensing platform for highly sensitive detection and simultaneous imaging of dual miRNAs in living cells.
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Affiliation(s)
- Xiang Xiong
- Department of General Surgery, Department of Burn and Plastic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Wenya Dang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ruxin Luo
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ying Long
- College of Biology, Hunan University, Changsha, 410082, China
| | - Chunyi Tong
- College of Biology, Hunan University, Changsha, 410082, China
| | - Liqin Yuan
- Department of General Surgery, Department of Burn and Plastic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha, 410082, China.
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19
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Deng J, Walther A. ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002629. [PMID: 32881127 DOI: 10.1002/adma.202002629] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.
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Affiliation(s)
- Jie Deng
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg, D-79110, Germany
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20
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Li Y, Liu J. Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers. Chemistry 2020; 26:13644-13651. [PMID: 32700427 DOI: 10.1002/chem.202001835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na+ -binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na+ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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21
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Liu Y, Le C, Tyrrell DL, Le XC, Li XF. Aptamer Binding Assay for the E Antigen of Hepatitis B Using Modified Aptamers with G-Quadruplex Structures. Anal Chem 2020; 92:6495-6501. [PMID: 32250595 DOI: 10.1021/acs.analchem.9b05740] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The e antigen of hepatitis B (HBeAg) is positively associated with an increased risk of developing liver cancer and cirrhosis in chronic hepatitis B (CHB) patients. Clinical monitoring of HBeAg provides guidance to the treatment of CHB and the assessment of disease progression. We describe here an affinity binding assay for HBeAg, which takes advantage of G-quadruplex aptamers for enhanced binding and stability. We demonstrate a strategy to improve the binding affinity of aptamers by modifying their sequences upon their G-quadruplex and secondary structures. On the basis of predicting a stable G-quadruplex and a secondary structure, we truncated 19 nucleotides (nt) from the primer regions of an 80-nt aptamer, and the resulting 61-nt aptamer enhanced binding affinity by 19 times (Kd = 1.2 nM). We mutated a second aptamer (40 nt) in one loop region and incorporated pyrrolo-deoxycytidine to replace deoxycytidine in another loop. The modified 40-nt aptamer, with a stable G-quadruplex and two modified loops, exhibited a 100 times higher binding affinity for HBeAg (Kd = 0.4 nM) than the unmodified original aptamer. Using the two newly modified aptamers, one serving as the capture and the other as the reporter, we have developed an improved sandwich binding assay for HBeAg. Analyses of HBeAg in serum samples (concentration ranging from 0.1 to 60 ng/mL) of 10 hepatitis B patients, showing consistent results with clinical tests, demonstrate a successful application of the aptamer modification strategy and the associated aptamer binding assay.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Connie Le
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada, T6G 2E1
| | - D Lorne Tyrrell
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada, T6G 2E1
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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22
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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23
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Miyagawa A, Okada Y, Okada T. Aptamer-Based Sensing of Small Organic Molecules by Measuring Levitation Coordinate of Single Microsphere in Combined Acoustic-Gravitational Field. ACS OMEGA 2020; 5:3542-3549. [PMID: 32118169 PMCID: PMC7045491 DOI: 10.1021/acsomega.9b03860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
We present aptamer-based sensing using a coupled acoustic-gravitational (CAG) field, which transduces a change in the density of a microparticle (MP) to a change in the levitation coordinate. A large density of the MP is initially induced by the binding of gold nanoparticles (AuNPs) on the MP through sandwich hybridization with aptamer DNA molecules. Targets added to the system interact with the aptamer DNA molecules to form complexes, and the duplex between the aptamer and the probe DNA molecules is dissociated. This leads to the release of AuNPs from the MP and a decrease in its density. As the target concentration increases, the levitation coordinate of the MP increases. From the levitation coordinate shift, we can determine the target concentration. The detection limits for adenosine triphosphate, dopamine, and ampicillin as test targets are 9.8 nM, 17 nM, and 160 pM, respectively. The dissociation constants for the aptamer-target complexes are quantitatively determined from the dependence of the levitation coordinate on the target concentration. This scheme is a useful analytical tool not only for the trace analyses of targets but also for the evaluation of aptamer-target interactions.
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24
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Wang H, Wang H, Zhang M, Jia Y, Li Z. A label-free aptamer-based biosensor for microRNA detection by the RNA-regulated fluorescence of malachite green. RSC Adv 2019; 9:32906-32910. [PMID: 35529731 PMCID: PMC9073149 DOI: 10.1039/c9ra07552f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) have been considered as promising molecular biomarkers for disease diagnosis, prognosis, as well as drug development. Herein, we wish to report a low background and label-free aptamer-based biosensor for miRNA assay by RNA-regulated fluorescence of malachite green (MG). In this biosensor-based strategy, target miRNA can specifically hybridize with the DNA extension template to form the T7 in vitro transcription system. Then the following transcription amplification produces a large number of MG RNA aptamers (MGAs) which light up the fluorescence of the MG, achieving significant fluorescence enhancement for miRNA quantitative analysis. The aptamer-based biosensor exhibits high sensitivity with a quite low detection limit of 10 amol target miRNA and high specificity to clearly discriminate very similar miRNA family members, even only one base difference. Furthermore, we have demonstrated that the biosensor is practical and reliable for the quantitative detection of miRNA in complex real samples.
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Affiliation(s)
- Honghong Wang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Hui Wang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Mai Zhang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Yuting Jia
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Zhengping Li
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
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25
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Seelam Prabhakar P, A Manderville R, D Wetmore S. Impact of the Position of the Chemically Modified 5-Furyl-2'-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer-Protein Complex: Structural Insights into Aptamer Response from MD Simulations. Molecules 2019; 24:molecules24162908. [PMID: 31405145 PMCID: PMC6720718 DOI: 10.3390/molecules24162908] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.
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Affiliation(s)
- Preethi Seelam Prabhakar
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AL T1K 3M4, Canada
| | - Richard A Manderville
- Department of Chemistry and Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AL T1K 3M4, Canada.
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He Y, Chang Y, Chen D, Liu J. Probing Local Folding Allows Robust Metal Sensing Based on a Na + -Specific DNAzyme. Chembiochem 2019; 20:2241-2247. [PMID: 30989776 DOI: 10.1002/cbic.201900143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Indexed: 12/26/2022]
Abstract
Fluorescent metal sensors based on DNA often rely on changes in end-to-end distance or local environmental near fluorophore labels. Because metal ions can also nonspecifically interact with DNA through various mechanisms, such as charge screening, base binding, and increase or decrease in duplex stability, robust and specific sensing of metal ions has been quite challenging. In this work, a side-by-side comparison of two signaling strategies on a Na+ -specific DNAzyme that contained a Na+ -binding aptamer was performed. The duplex regions of the DNAzyme was systematically shortened and its effect was studied by using a 2-aminopurine (2AP)-labeled substrate strand. Na+ binding affected the local environmental of the 2AP label and increased its fluorescence. A synergistic process of Na+ binding and forming the duplex on the 5'-end of the enzyme strand was observed, and this end was close to the aptamer loop. Effective Na+ binding was achieved with a five base-pair stem. The effect on the 3'-end is more continuous, and the stem needs to form first before Na+ can bind. With an optimized substrate binding arm, a FRET-based sensor has been designed by labeling the two ends of a cis form of the DNAzyme with two fluorophores. In this case, Na+ failed to show a distinct difference from that of Li+ or K+ ; thus indicating that probing changes to the local environment allows more robust sensing of metal ions.
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Affiliation(s)
- Yanping He
- State Key Laboratory of Precision Measurement Technology and, Instruments, Tianjin University, Tianjin, 300072, P.R. China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Yangyang Chang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering, (Ministry of Education), Dalian University of Technology, Dalian, 116024, P.R. China
| | - Da Chen
- State Key Laboratory of Precision Measurement Technology and, Instruments, Tianjin University, Tianjin, 300072, P.R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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27
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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Ma X, Qiao S, Sun H, Su R, Sun C, Zhang M. Development of Structure-Switching Aptamers for Kanamycin Detection Based on Fluorescence Resonance Energy Transfer. Front Chem 2019; 7:29. [PMID: 30792976 PMCID: PMC6374352 DOI: 10.3389/fchem.2019.00029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/11/2019] [Indexed: 12/21/2022] Open
Abstract
The structure-switching aptamers are designed for the simple and rapid detection of kanamycin based on the signal transduction principle of fluorescence resonance energy transfer (FRET). The structure switch is composed of kanamycin-binding aptamers and the complementary strands, respectively labeled with fluorophore and quencher, denoted as FDNA and QDNA. In the absence of kanamycin, FDNA and QDNA form the double helix structure through the complementary pairing of bases. The fluorophore and the quencher are brought into close proximity, which results in the fluorescence quenching because of the FRET mechanism. In the presence of kanamycin, the FDNA specifically bind to the target due to the high affinity of aptamers, and the QDNA are dissociated. The specific recognition between aptamers and kanamycin will obstruct the formation of structure switch and reduce the efficiency of FRET between FDNA and QDNA, thus leading to the fluorescence enhancement. Therefore, based on the structure-switching aptamers, a simple fluorescent assay for rapid detection of kanamycin was developed. Under optimal conditions, there was a good linear relationship between kanamycin concentration and the fluorescence signal recovery. The linear range of this method in milk samples was 100-600 nM with the detection limit of 13.52 nM (3σ), which is well below the maximum residue limit (MRL) of kanamycin in milk. This method shows excellent selectivity for kanamycin over the other common antibiotics. The structure-switching aptamers have been successfully applied to the detection of kanamycin spiked in milk samples with the satisfying recoveries between 101.3 and 109.1%, which is well-consistent with the results from LC-MS/MS. Due to the outstanding advantages of facile operation, rapid detection, high sensitivity, excellent specificity, and low cost, the application and extension of this strategy for rapid determination of antibiotics in food samples may greatly improve the efficiency in food safety and quality supervision.
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Affiliation(s)
- Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Shangna Qiao
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Hongjing Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Ruifang Su
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, China
| | - Mingdi Zhang
- Department of Food Science and Engineering, College of Food Science and Engineering, Jilin University, Changchun, China
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29
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Özyurt C, Canbay ZÇ, Dinçkaya E, Evran S. A highly sensitive DNA aptamer-based fluorescence assay for sarcosine detection down to picomolar levels. Int J Biol Macromol 2019; 129:91-97. [PMID: 30738156 DOI: 10.1016/j.ijbiomac.2019.02.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/23/2022]
Abstract
Sarcosine is an amino acid derivative, which is considered as a key metabolite in various metabolic processes. Therefore, simple and sensitive detection methods are needed for further understanding its metabolic role and diagnostic value. In this study, we developed a novel method that meets the need for practical and sensitive detection in a complex medium mimicking urine conditions. For this aim, we selected sarcosine-specific DNA aptamers using graphene oxide-assisted systemic evolution of ligands by exponential enrichment (GO-SELEX). The candidate aptamers were labeled with 6-carboxyfluorescein (6-FAM) at their 5' ends. Two aptamers, namely 9S and 13S produced a significant fluorescence signal upon sarcosine binding. Both aptamers enabled a sensitive analysis with a detection limit of 0.5 pM. The linear detection ranged between 5 pM and 50 μM for 9S aptamer, while 13S aptamer enabled a wider linear detection range between 5 pM and 500 μM. The aptamer-based assay allowed rapid detection with no need for chemical derivatization of sarcosine and sophisticated instruments. Moreover, the aptamer-based assay was free of interference from urea and human serum albumin.
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Affiliation(s)
- Canan Özyurt
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey
| | - Zeynep Çelik Canbay
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey
| | - Erhan Dinçkaya
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova-İzmir, Turkey.
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30
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Yan Q, Ding XY, Chen ZH, Xue SF, Han XY, Lin ZY, Yang M, Shi G, Zhang M. pH-Regulated Optical Performances in Organic/Inorganic Hybrid: A Dual-Mode Sensor Array for Pattern-Recognition-Based Biosensing. Anal Chem 2018; 90:10536-10542. [PMID: 30099878 DOI: 10.1021/acs.analchem.8b02603] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dual-mode optical assays are becoming more popular and attractive because they would provide robust detailed information in biochemical analysis. We herein unveil a novel dual-mode optical (i.e., UV-vis absorption and fluorescence) method for multifunctional sensing of phosphate compounds (PCs) (e.g., nucleotides and pyrophosphate) based on pattern recognition, which innovatively employs only one kind of porphyrin/lanthanide-doped upconversion nanoparticles (Ln-UCNPs) hybrid integrated with a facile pH-regulated strategy as the sensor array. An easy-to-obtain porphyrin hydrate (tetraphenylporphyrin tetrasulfonic acid hydrate, TPPS) can assemble onto the ligand-free Ln-UCNPs to construct the organic/inorganic hybrid (TPPS/Ln-UCNPs), leading to a new absorption band to quench the upconversion fluorescence of Ln-UCNPs due to fluorescence resonance energy transfer (FRET). The dual-mode optical performances of TPPS/Ln-UCNPs are characteristically correlated with the pH in aqueous solution. Thus, as a proof-of-concept design, three types of TPPS/Ln-UCNPs (TPPS/Ln-UCNPs4, TPPS/Ln-UCNPs4.5, and TPPS/Ln-UCNPs5) were prepared by using buffers with different pH (at 4, 4.5, and 5) to form our proposed sensor array, which would result in individual dual-mode optical response patterns upon being challenged with PCs for their pattern recognition through a competitive mechanism between TPPS and PCs. The results show that three TPPS/Ln-UCNPs n sensors can successfully permit the sensitive detection of 14 PCs and differentiate them between different concentrations, as well as a mixture of them. The pH-dependent TPPS/Ln-UCNPs promises the simple, yet powerful discrimination of PCs via pattern recognition, would prospectively stimulate and expand the use of organic/inorganic hybrid toward more biosensing applications.
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Affiliation(s)
- Qing Yan
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Xu-Yin Ding
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Zi-Han Chen
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Shi-Fan Xue
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Xin-Yue Han
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Zi-Yang Lin
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Miao Yang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
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31
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Tan Z, Heemstra JM. High-Throughput Measurement of Small-Molecule Enantiopurity by Using Flow Cytometry. Chembiochem 2018; 19:1853-1857. [PMID: 30126025 DOI: 10.1002/cbic.201800341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Fluorescence-activated cell sorting (FACS) offers a powerful approach to high-throughput library screening in directed evolution experiments. However, FACS is rarely used in the evolution of stereoselective enzymes, due to the difficulty of designing fluorescence-based assays for measuring enantiopurity. Here, we describe a new FACS-based enantiopurity analysis approach that overcomes these limitations by using enantiomeric DNA biosensors labeled with orthogonal fluorophores. By co-encapsulating the biosensors with a mixture of target enantiomers in microfluidic droplets, we could demonstrate the use of FACS to differentiate between droplets having various levels of target enantiopurity. We envision the utility of this method for high-throughput screening of enantiopurity in the directed evolution of stereoselective enzymes, thereby facilitating the discovery of new asymmetric biocatalysts for the synthesis of pharmaceuticals and other high-value chemicals.
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Affiliation(s)
- Zhesen Tan
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.,Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
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32
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Pan W, Liu B, Gao X, Yu Z, Liu X, Li N, Tang B. A graphene-based fluorescent nanoprobe for simultaneous monitoring of miRNA and mRNA in living cells. NANOSCALE 2018; 10:14264-14271. [PMID: 30010689 DOI: 10.1039/c8nr04106g] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Since microRNA-21 (miR-21) and protein programmed cell death 4 (PDCD4) are implicated in tumor progression, simultaneous monitoring of the dynamic variation of miR-21 and PDCD4 mRNA in living cells is of great interest for understanding their relationship in the pathology of the disease. Herein, a versatile nanoprobe based on graphene oxide (GO) and DNA was prepared which can simultaneously monitor and visualize miR-21 and PDCD4 mRNA in living cells. In vitro experiments demonstrate that the nanoprobe exhibits outstanding selectivity and high sensitivity towards miR-21 and PDCD4 mRNA. Moreover, by exploiting the DNA/GO sensing platform, simultaneous imaging of miR-21 and PDCD4 mRNA in MCF-7 human breast cancer cells has been realized. More significantly, an inverse correlation between miR-21 and PDCD4 mRNA was verified by fluorescence confocal imaging and RT-PCR results, indicating the distinguishing ability of the nanoprobe at various expression levels of RNAs. The current strategy provides a promising tool to implement the detection of miR-21 and PDCD4 mRNA in cancer cells and can be expected to be applied for other biomolecular sensing.
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Affiliation(s)
- Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Bo Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Xiaonan Gao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Zhengze Yu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Xiaohan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
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33
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Tsuchiya A, Hashim SN, Ise S, Furuhata T, Kawai K, Wakabayashi R, Goto M, Kamiya N, Sando S. BODIPY-labeled Fluorescent Aptamer Sensors for Turn-on Sensing of Interferon-gamma and Adenine Compounds on Cells. ANAL SCI 2018; 32:543-7. [PMID: 27169654 DOI: 10.2116/analsci.32.543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-γ and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a turn-on detection of the target molecule with improved off/on efficiency.
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Affiliation(s)
- Akira Tsuchiya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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34
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Phan DT, Jin L, Wustoni S, Chen CH. Buffer-free integrative nanofluidic device for real-time continuous flow bioassays by ion concentration polarization. LAB ON A CHIP 2018; 18:574-584. [PMID: 29299579 DOI: 10.1039/c7lc01066d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To perform precision medicine in real-time, a sensor capable of continuously monitoring target biomolecules secreted from a patient under dynamic situations is essential. In this study, a novel portable device combining an aptamer probe and a nanofluidic component was developed, enabling the buffer-free continuous monitoring of small molecules in biological fluids. This integration is synergistic: the aptamer sensor is used to bind target biomolecules, triggering a fluorescence signal change, while the nanofluidic component is applied to achieve ion concentration polarization and convert serum into a clean buffer for aptamer signal regeneration. To demonstrate the system's versatility, we measured various adenosine triphosphate concentrations in human serum for hours with high sensitivity and specificity at minute temporal resolution. Our results demonstrate that this integrative device can be applied for the continuous measurement of target biomolecules and online signal regeneration in patient samples without the use of bulky clean buffer solutions for dynamic real-time healthcare.
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Affiliation(s)
- Dinh-Tuan Phan
- Department of Biomedical Engineering, National University of Singapore, 7 Engineering Drive 1, Singapore 117574.
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35
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Guo X, Ye T, Liu L, Hu X. Preparation and characterization of an aptamer-functionalized solid-phase microextraction fiber and its application in the selective monitoring of adenosine phosphates with liquid chromatography and tandem mass spectrometry. J Sep Sci 2018; 39:1533-41. [PMID: 27106768 DOI: 10.1002/jssc.201501264] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 11/08/2022]
Abstract
An aptamer with adenosine triphosphate as a ligand was immobilized onto the surface of a porous-polymer-coated fiber to obtain an aptamer-functionalized porous-polymer-coated solid-phase microextraction fiber. The fiber was observed with a crosslinked and porous morphological surface structure. It shows specific selectivity to adenosine triphosphate with a selectivity coefficient of 22.1 compared to the scrambled oligonucleotide functionalized fiber, and the selectivity factors over other analogues and reference compounds were from 6.1 to 77.5. When the fiber-based solid-phase microextraction was coupled with liquid chromatography and tandem mass spectrometry, detection limits of 2.7, 29, and 34 μg/L were achieved for adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate, respectively. The spiking recoveries of 77.6-91.9% were achieved for trace adenosine phosphates in human serum sample. Furthermore, the fibers showed high stability and good reusability and could be used over 50 times for the real serum sample pretreatment without remarkable performance reduction.
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Affiliation(s)
- Xuan Guo
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
| | - Tingting Ye
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
| | - Luying Liu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
| | - Xiaogang Hu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
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36
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Wei B, Zhang J, Ou X, Lou X, Xia F, Vallée-Bélisle A. Engineering Biosensors with Dual Programmable Dynamic Ranges. Anal Chem 2018; 90:1506-1510. [PMID: 29300471 DOI: 10.1021/acs.analchem.7b04852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although extensively used in all fields of chemistry, molecular recognition still suffers from a significant limitation: host-guest binding displays a fixed, hyperbolic dose-response curve, which limits its usefulness in many applications. Here we take advantage of the high programmability of DNA chemistry and propose a universal strategy to engineer biorecognition-based sensors with dual programmable dynamic ranges. Using DNA aptamers as our model recognition element and electrochemistry as our readout signal, we first designed a dual signaling "signal-on" and "signal-off" adenosine triphosphate (ATP) sensor composed of a ferrocene-labeled ATP aptamer in complex to a complementary, electrode-bound, methylene-blue labeled DNA. Using this simple "dimeric" sensor, we show that we can easily (1) tune the dynamic range of this dual-signaling sensor through base mutations on the electrode-bound DNA, (2) extend the dynamic range of this sensor by 2 orders of magnitude by using a combination of electrode-bound strands with varying affinity for the aptamers, (3) create an ultrasensitive dual signaling sensor by employing a sequestration strategy in which a nonsignaling, high affinity "depletant" DNA aptamer is added to the sensor surface, and (4) engineer a sensor that simultaneously provides extended and ultrasensitive readouts. These strategies, applicable to a wide range of biosensors and chemical systems, should broaden the application of molecular recognition in various fields of chemistry.
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Affiliation(s)
- Benmei Wei
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Juntao Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Xiaowen Ou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Xiaoding Lou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Fan Xia
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Alexis Vallée-Bélisle
- Laboratory Biosensors & Nanomachines, Département de Chimie, Université de Montréal , Montréal, Québec H3T 1J4, Canada
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37
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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Morii T. A Bioorganic Chemistry Approach to Understanding Molecular Recognition in Protein–Nucleic Acid Complexes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011
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Zhang Z, Oni O, Liu J. New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection. Nucleic Acids Res 2017; 45:7593-7601. [PMID: 28591844 PMCID: PMC5737652 DOI: 10.1093/nar/gkx517] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 06/01/2017] [Indexed: 11/27/2022] Open
Abstract
The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed. The number of binding sites can also be increased, and up to four sites are introduced in a single DNA sequence. Finally, the different sequences are made into fluorescent biosensors based on the structure-switching signaling aptamer design. The one-site aptamer has 3.8-fold higher sensitivity at lower adenosine concentration with a limit of detection of 9.1 μM adenosine, but weaker fluorescence signal at higher adenosine concentrations, consistent with a moderate cooperativity in the original aptamer. This work has offered insights into a classic aptamer for the relationship between the number of binding sites and sensitivity, and a shorter aptamer for improved biosensor design.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Olatunji Oni
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Zhang S, Geryak R, Geldmeier J, Kim S, Tsukruk VV. Synthesis, Assembly, and Applications of Hybrid Nanostructures for Biosensing. Chem Rev 2017; 117:12942-13038. [DOI: 10.1021/acs.chemrev.7b00088] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Liu J, Cui M, Niu L, Zhou H, Zhang S. Enhanced Peroxidase-Like Properties of Graphene-Hemin-Composite Decorated with Au Nanoflowers as Electrochemical Aptamer Biosensor for the Detection of K562 Leukemia Cancer Cells. Chemistry 2016; 22:18001-18008. [DOI: 10.1002/chem.201604354] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers; College of Chemistry and Chemical Engineering; Linyi University; Linyi 276005 P.R. China
| | - Meirong Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers; College of Chemistry and Chemical Engineering; Linyi University; Linyi 276005 P.R. China
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong; Shandong Normal University; Jinan 250014 P.R. China
| | - Li Niu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers; College of Chemistry and Chemical Engineering; Linyi University; Linyi 276005 P.R. China
| | - Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers; College of Chemistry and Chemical Engineering; Linyi University; Linyi 276005 P.R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers; College of Chemistry and Chemical Engineering; Linyi University; Linyi 276005 P.R. China
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Carrillo-Carrion C, Escudero A, Parak WJ. Optical sensing by integration of analyte-sensitive fluorophore to particles. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Tang J, Shi H, He X, Lei Y, Guo Q, Wang K, Yan L, He D. Tumor cell-specific split aptamers: target-driven and temperature-controlled self-assembly on the living cell surface. Chem Commun (Camb) 2016; 52:1482-5. [PMID: 26660498 DOI: 10.1039/c5cc08977h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An activatable split aptamer probe with target-induced shape change and thermosensitivity was developed. Triggered by proteins on the cell surface, the probe could assemble into a desired binding shape, thus affording a FRET-based tumor cell assay. Moreover, a reversible cell catch/release strategy was realized through mild temperature switching (4°C/37°C).
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Affiliation(s)
- Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Qiuping Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Lv'an Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha, 410082, China.
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Wang H, Peng P, Liu S, Li T. Thioflavin T behaves as an efficient fluorescent ligand for label-free ATP aptasensor. Anal Bioanal Chem 2016; 408:7927-7934. [PMID: 27682839 DOI: 10.1007/s00216-016-9926-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 12/22/2022]
Abstract
Here, we for the first time demonstrated thioflavin T (ThT) as an efficient fluorescent ligand for 27-mer ATP-binding aptamer (ABA27), providing a novel signal readout mode for label-free selective ATP detection. ABA27 can promote the fluorescence emission of ThT with an unprecedentedly high efficiency, attributed to the specific structure of ABA27 rather than the G-tracts. Polyacrylamide gel electrophoresis, fluorescence spectroscopy, and fluorometric titration reveal that ThT interacts with ABA27 with a lower binding affinity (Kd ~89 μM) than ATP, which allows ATP to easily compete with ThT for the DNA binder. In the presence of ThT, adding ATP induces ABA27 to undergo a structural change, thereby not favoring the binding to ThT, verified by circular dichroism and UV-Vis absorption spectroscopy. As a result, the fluorescence intensity of ThT decreases dramatically, enabling the sensitive detection of ATP with high selectivity over other analogs. Such a sensing strategy may make ThT able to serve as a facile signal reporter for DNA nanomechanical devices fueled with ATP. Graphical Abstract The principle of the displacement of ThT by ATP.
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Affiliation(s)
- Huihui Wang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China
| | - Pai Peng
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China
| | - Shuangna Liu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China
| | - Tao Li
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China.
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Kato T, Shimada I, Kimura R, Hyuga M. Light-up fluorophore--DNA aptamer pair for label-free turn-on aptamer sensors. Chem Commun (Camb) 2016; 52:4041-4. [PMID: 26891088 DOI: 10.1039/c5cc08816j] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a light-up fluorophore-DNA aptamer pair for label-free aptamer sensors that fluoresce upon binding to the analyte. A 42mer DNA aptamer binding to the environment-sensitive fluorophore, dapoxyl, which increased the fluorescence by more than 700-fold upon binding, was successfully used to construct aptamer sensors by fusion with analyte-binding DNA aptamers.
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Affiliation(s)
- Teru Kato
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Ippei Shimada
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Ryota Kimura
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Masumi Hyuga
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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48
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Das P, Reches M. Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex. NANOSCALE 2016; 8:9527-36. [PMID: 26730518 DOI: 10.1039/c5nr07714a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.
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Affiliation(s)
- Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. and The Centre for Nanoscience and Nanotechnology. The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. and The Centre for Nanoscience and Nanotechnology. The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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49
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Affiliation(s)
- Dae-Ro Ahn
- Life Sciences Research Division, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650, South Korea
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50
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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