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Abstract
The systematic evolution of ligands by exponential enrichment (SELEX) enables the identification of ssDNA or RNA sequences binding to different target molecules, highly specific and with high affinity. In this chapter, we describe a selection strategy with ssDNA for a histidine-tagged protein that could be either performed hands-on manually or fully automated by an appropriate robotic selection platform.
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Affiliation(s)
- Stefan Breuers
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany.
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2
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Amini R, Zhang Z, Li J, Gu J, Brennan J, Li Y. Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments. ANALYSIS & SENSING 2022; 2:e202200012. [PMID: 35574520 PMCID: PMC9082509 DOI: 10.1002/anse.202200012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/19/2022] [Indexed: 12/17/2022]
Abstract
The SARS‐CoV‐2 virus and COVID‐19 pandemic continue to demand effective diagnostic and therapeutic solutions. Finding these solutions requires highly functional molecular recognition elements. Nucleic acid aptamers represent a possible solution. Characterized by their high affinity and specificity, aptamers can be rapidly identified from random‐sequence nucleic acid libraries. Over the past two years, many labs around the world have rushed to create diverse aptamers that target two important structural proteins of SARS‐CoV‐2: the spike (S) protein and nucleocapsid (N) protein. These have led to the identification of many aptamers that show real promise for the development of diagnostic tests and therapeutic agents for SARS‐CoV‐2. Herein we review all these developments, with a special focus on the development of diverse aptasensors for detecting SARS‐CoV‐2. These include electrochemical and optical sensors, lateral flow devices, and aptamer‐linked immobilized sorbent assays.
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Affiliation(s)
- Ryan Amini
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jiuxing Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - John Brennan
- McMaster University Biointerfaces Institute CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences 1280 Main Street West L8S4K1 Hamilton CANADA
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3
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Ozturk M, Nilsen-Hamilton M, Ilgu M. Aptamer Applications in Neuroscience. Pharmaceuticals (Basel) 2021; 14:1260. [PMID: 34959661 PMCID: PMC8709198 DOI: 10.3390/ph14121260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges.
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Affiliation(s)
- Meric Ozturk
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Marit Nilsen-Hamilton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
| | - Muslum Ilgu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021; 60:16800-16823. [PMID: 33559947 PMCID: PMC8292151 DOI: 10.1002/anie.202008663] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
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Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G. A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:10367-10373. [PMID: 34230708 PMCID: PMC8250900 DOI: 10.1002/ange.202100316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 12/14/2022]
Abstract
The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS-CoV-2 (CoV2-S) binds to the human angiotensin-converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2-S. The aptamer does not bind to the RBD of CoV2-S and does not block the interaction of CoV2-S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS-CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.
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Affiliation(s)
- Anton Schmitz
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Anna Weber
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Mehtap Bayin
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Stefan Breuers
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Volkmar Fieberg
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Michael Famulok
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Günter Mayer
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
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Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G. A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism*. Angew Chem Int Ed Engl 2021; 60:10279-10285. [PMID: 33683787 DOI: 10.1101/2020.12.23.424171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 05/25/2023]
Abstract
The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS-CoV-2 (CoV2-S) binds to the human angiotensin-converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2-S. The aptamer does not bind to the RBD of CoV2-S and does not block the interaction of CoV2-S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS-CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.
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Affiliation(s)
- Anton Schmitz
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Anna Weber
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Mehtap Bayin
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Stefan Breuers
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Volkmar Fieberg
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Michael Famulok
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G. A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism*. Angew Chem Int Ed Engl 2021; 60:10279-10285. [PMID: 33683787 PMCID: PMC8251191 DOI: 10.1002/anie.202100316] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 11/24/2022]
Abstract
The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS-CoV-2 (CoV2-S) binds to the human angiotensin-converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2-S. The aptamer does not bind to the RBD of CoV2-S and does not block the interaction of CoV2-S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS-CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.
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Affiliation(s)
- Anton Schmitz
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Anna Weber
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Mehtap Bayin
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Stefan Breuers
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Volkmar Fieberg
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Michael Famulok
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Günter Mayer
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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