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Evtugyn G, Porfireva A, Tsekenis G, Oravczova V, Hianik T. Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety. SENSORS (BASEL, SWITZERLAND) 2022; 22:3684. [PMID: 35632093 PMCID: PMC9143886 DOI: 10.3390/s22103684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics are often used in human and veterinary medicine for the treatment of bacterial diseases. However, extensive use of antibiotics in agriculture can result in the contamination of common food staples such as milk. Consumption of contaminated products can cause serious illness and a rise in antibiotic resistance. Conventional methods of antibiotics detection such are microbiological assays chromatographic and mass spectroscopy methods are sensitive; however, they require qualified personnel, expensive instruments, and sample pretreatment. Biosensor technology can overcome these drawbacks. This review is focused on the recent achievements in the electrochemical biosensors based on nucleic acid aptamers for antibiotic detection. A brief explanation of conventional methods of antibiotic detection is also provided. The methods of the aptamer selection are explained, together with the approach used for the improvement of aptamer affinity by post-SELEX modification and computer modeling. The substantial focus of this review is on the explanation of the principles of the electrochemical detection of antibiotics by aptasensors and on recent achievements in the development of electrochemical aptasensors. The current trends and problems in practical applications of aptasensors are also discussed.
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Affiliation(s)
- Gennady Evtugyn
- A.M. Butlerov’ Chemistry Institute, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (G.E.); (A.P.)
- Analytical Chemistry Department, Chemical Technology Institute, Ural Federal University, 19 Mira Street, 620002 Ekaterinburg, Russia
| | - Anna Porfireva
- A.M. Butlerov’ Chemistry Institute, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (G.E.); (A.P.)
| | - George Tsekenis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece;
| | - Veronika Oravczova
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska Dolina F1, 842 48 Bratislava, Slovakia;
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska Dolina F1, 842 48 Bratislava, Slovakia;
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Chakraborty B, Das S, Gupta A, Xiong Y, Vyshnavi TV, Kizer ME, Duan J, Chandrasekaran AR, Wang X. Aptamers for Viral Detection and Inhibition. ACS Infect Dis 2022; 8:667-692. [PMID: 35220716 PMCID: PMC8905934 DOI: 10.1021/acsinfecdis.1c00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Indexed: 02/07/2023]
Abstract
Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.
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Affiliation(s)
- Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sreyashi Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Arushi Gupta
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - T-V Vyshnavi
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jinwei Duan
- Department of Chemistry and Materials Science, Chang’an University, Xi’an, Shaanxi 710064, China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Vinod SP, Vignesh R, Priyanka M, Tirumurugaan KG, Sivaselvam SN, Raj GD. Generation of single stranded DNA with selective affinity to bovine spermatozoa. Anim Biosci 2021; 34:1579-1589. [PMID: 32882770 PMCID: PMC8495356 DOI: 10.5713/ajas.20.0235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 07/23/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions. METHODS A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer. The enriched nucleotides were predicted for secondary structures by Mfold, motifs by Multiple Em for Motif Elicitation and 5' labelled with biotin/6-FAM to determine the binding potential and binding pattern. RESULTS We generated 14.1 and 17.7 million reads from sixth and seventh rounds of SELEX respectively to bovine spermatozoa. The CD-HIT clustered 78,098 and 21,196 reads in the top ten clusters and FASTAptamer identified 2,195 and 4,405 unique sequences in the top three clusters from the sixth and seventh rounds, respectively. The identified oligonucleotides formed secondary structures with delta G values between -1.17 to -26.18 kcal/mol indicating varied stability. Confocal imaging with the oligonucleotides from the seventh round revealed different patterns of binding to bovine spermatozoa (fluorescence of the whole head, spot of fluorescence in head and mid- piece and tail). Use of a 5'-biotin tagged oligonucleotide from the sixth round at 100 pmol with 4×106 spermatozoa could trap almost 80% from the suspension. CONCLUSION The binding patterns and ability of the identified oligonucleotides confirms successful optimization of the SELEX process and generation of aptamers to bovine spermatozoa. These oligonucleotides provide a quick approach for selective capture of spermatozoa from complex samples. Future SELEX rounds with X- or Y- enriched sperm suspension will be used to generate oligonucleotides that bind to spermatozoa of a specific sex type.
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Affiliation(s)
- Sivadasan Pathiyil Vinod
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai – 600051, India
| | - Rajamani Vignesh
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai – 600051, India
| | - Mani Priyanka
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai – 600051, India
| | - Krishnaswamy Gopalan Tirumurugaan
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai – 600051, India
| | - Salem Nagalingam Sivaselvam
- Department of Animal Genetics and Breeding, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai – 600051, India
| | - Gopal Dhinakar Raj
- Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai – 600051, India
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Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020; 21:E8774. [PMID: 33233573 PMCID: PMC7699794 DOI: 10.3390/ijms21228774] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia; (D.B.); (A.K.)
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Wang T, Yin W, AlShamaileh H, Zhang Y, Tran PHL, Nguyen TNG, Li Y, Chen K, Sun M, Hou Y, Zhang W, Zhao Q, Chen C, Zhang PZ, Duan W. A Detailed Protein-SELEX Protocol Allowing Visual Assessments of Individual Steps for a High Success Rate. Hum Gene Ther Methods 2020; 30:1-16. [PMID: 30700146 DOI: 10.1089/hgtb.2018.237] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As a nucleic acid alternative to traditional antibody, aptamer holds great potential in various fields of biology and medicine such as targeted gene therapy, drug delivery, bio-sensing, and laboratory medicine. Over the past decades, the conventional Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method has undergone dramatic modifications and improvements owing to developments in material sciences and analytical techniques. However, many of the recently developed strategies either require complex materials and instruments or suffer from low efficiency and high failure rates in the selection of desired aptamers. Accordingly, the development of aptamers against new or novel targets is still a major obstacle for aptamer-based research and application. Here, an improved protein-SELEX procedure is presented for simplified and highly efficient isolation of aptamers against protein targets. Approaches are described that ensure a high success rate in aptamer selection by simplifying polymerase chain reaction procedures, introducing denature gel, utilizing an electro-elution-based single-stranded DNA separation strategy, as well as an enzyme-linked immunosorbent assay-based highly sensitive binding assay. In addition, a simplified sample preparation method for MiSeq-based next-generation sequencing is also introduced. While a recombinant protein as a bait protein for SELEX is discussed here, this protocol will also be invaluable for researchers wishing to develop aptamers against targets other than proteins such as small molecules, lipids, carbohydrates, cells, and micro-organisms for future gene therapy and/or diagnostics.
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Affiliation(s)
- Tao Wang
- 1 School of Nursing, Zhengzhou University, Zhengzhou, P.R. China.,2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia
| | - Wang Yin
- 2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia
| | - Hadi AlShamaileh
- 2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia
| | - Yumei Zhang
- 2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia
| | - Phuong Ha-Lien Tran
- 2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia
| | - Tuong Ngoc-Gia Nguyen
- 2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia
| | - Yong Li
- 3 Cancer Care Centre, St. George Hospital, Kogarah, and St. George and Sutherland Clinical School, University of New South Wales, Kensington, Australia
| | - Kuisheng Chen
- 4 Department of Pathology, The First Affiliated Hospital, Zhengzhou University, He'nan Key Laboratory of Tumor Pathology, Zhengzhou, P.R. China
| | - Miaomiao Sun
- 5 Department of Pathology, Affiliated Caner Hospital of Zhengzhou University and He'nan Cancer Hospital, Zhengzhou, P.R. China
| | - Yingchun Hou
- 6 Co-Innovation Center for Qinba Region Sustainable Development, Institute of Sports and Exercise Biology, Shaanxi Normal University, Xi'an, P.R. China
| | - Weihong Zhang
- 1 School of Nursing, Zhengzhou University, Zhengzhou, P.R. China
| | - Qingxia Zhao
- 1 School of Nursing, Zhengzhou University, Zhengzhou, P.R. China
| | - Changying Chen
- 1 School of Nursing, Zhengzhou University, Zhengzhou, P.R. China
| | - Pei-Zhuo Zhang
- 7 Suzhou GenePharma, Suzhou, P.R. China.,8 GenePharma-Deakin Joint Laboratory of Aptamer Medicine, Suzhou, P.R. China and Waurn Ponds, Victoria, Australia
| | - Wei Duan
- 2 School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Australia.,8 GenePharma-Deakin Joint Laboratory of Aptamer Medicine, Suzhou, P.R. China and Waurn Ponds, Victoria, Australia
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6
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Li Y, Lee JS. Recent developments in affinity-based selection of aptamers for binding disease-related protein targets. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00842-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Rani R, Yaseen AM, Malwade A, Sevilimedu A. An RNA aptamer to HP1/Swi6 facilitates heterochromatin formation at an ectopic locus in S.pombe. RNA Biol 2019; 16:742-753. [PMID: 30794054 DOI: 10.1080/15476286.2019.1584026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe (S.pombe), heterochromatin domains are established and maintained by protein complexes that contain numerous RNA binding domains among their components. The fission yeast HP1 protein Swi6 is one such component and contains an unstructured RNA-binding hinge, which is important for the integrity and silencing of heterochromatin. In this study, we have used an RNA aptamer that likely binds to the Swi6 hinge with high affinity, as a tool to perturb the natural interactions mediated by this domain. When the hinge is blocked by the aptamer RNA, Swi6 appears to become less restricted to the pericentromeres and is enriched at specific euchromatic loci. This suggests a role for the Swi6 hinge, along with the chromoshadow domain (previously shown) in controlling the spread of heterochromatin in S.pombe. The study also highlights the potential of using a synthetic aptamer RNA as a tool to perturb nucleic acid - protein interaction in vivo with the objective of understanding the functional relevance of such an interaction.
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Affiliation(s)
- Rita Rani
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Abdul Mohd Yaseen
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Akshay Malwade
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Aarti Sevilimedu
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
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Wang T, Chen C, Larcher LM, Barrero RA, Veedu RN. Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development. Biotechnol Adv 2018; 37:28-50. [PMID: 30408510 DOI: 10.1016/j.biotechadv.2018.11.001] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/28/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023]
Abstract
Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.
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Affiliation(s)
- Tao Wang
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia; School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Changying Chen
- School of Nursing, Zhengzhou University & Nursing Department, The First Affiliated Hospital of Zheng Zhou University, Zhengzhou 450001, China
| | - Leon M Larcher
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University, Perth 6150, Australia; Perron Institute for Neurological and Translational Science, Perth 6009, Australia.
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Eisold A, Labudde D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules 2018; 23:molecules23071690. [PMID: 29997341 PMCID: PMC6100600 DOI: 10.3390/molecules23071690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022] Open
Abstract
Micro-pollutants such as 17β-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. Aptamers are established as a possible detection tool, but the underlying ligand binding is largely unexplored. In this study, a previously described 35-mer E2-specific aptamer was used to analyse the binding characteristics between E2 and the aptamer with a MD simulation in an aqueous medium. Because there is no 3D structure information available for this aptamer, it was modeled using coarse-grained modeling method. The E2 ligand was positioned inside a potential binding area of the predicted aptamer structure, the complex was used for an 25 ns MD simulation, and the interactions were examined for each time step. We identified E2-specific bases within the interior loop of the aptamer and also demonstrated the influence of frequently underestimated water-mediated hydrogen bonds. The study contributes to the understanding of the behavior of ligands binding with aptamer structure in an aqueous solution. The developed workflow allows generating and examining further appealing ligand-aptamer complexes.
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Affiliation(s)
- Alexander Eisold
- Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
- Institute for Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany.
| | - Dirk Labudde
- Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
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Identification and characterization of nucleobase-modified aptamers by click-SELEX. Nat Protoc 2018; 13:1153-1180. [PMID: 29700486 DOI: 10.1038/nprot.2018.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aptamers are single-stranded oligonucleotides that are in vitro-selected to recognize their target molecule with high affinity and specificity. As they consist of the four canonical nucleobases, their chemical diversity is limited, which in turn limits the addressable target spectrum. Introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of the DNA and thereby the target spectrum. Here, we describe a protocol to select nucleobase-modified aptamers by using click chemistry (CuAAC) to introduce the preferred chemical modification. The use of click chemistry to modify the DNA library enables the introduction of a wide range of possible functionalities, which can be customized to the requirements of the target molecule and the desired application. This protocol yields modified DNA aptamers with extended interaction properties that are not accessible with the canonical set of nucleotides. After synthesis of the starting library containing a commercially available, alkyne-modified uridine (5-ethynyl-deoxyuridine (EdU)) instead of thymidine, the library is functionalized with the modification of choice by CuAAC. The thus-modified DNA is incubated with the target molecule and the best binding sequences are recovered. The chemical modification is removed during the amplification process. Therefore, this protocol is compatible with conventional amplification procedures and avoids enzymatic incompatibility problems associated with more extensive nucleobase modifications. After single-strand generation, the modification is reintroduced into the enriched library, which can then be subjected to the subsequent selection cycle. The duration of each selection cycle as outlined in the protocol is ∼1 d.
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Aptamer-siRNA Chimeras: Discovery, Progress, and Future Prospects. Biomedicines 2017; 5:biomedicines5030045. [PMID: 28792479 PMCID: PMC5618303 DOI: 10.3390/biomedicines5030045] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 02/07/2023] Open
Abstract
Synthetic nucleic acid ligands (aptamers) have emerged as effective delivery tools for many therapeutic oligonucleotide-based drugs, including small interfering RNAs (siRNAs). In this review, we summarize recent progress in the aptamer selection technology that has made possible the identification of cell-specific, cell-internalizing aptamers for the cell-targeted delivery of therapeutic oligonucleotides. In addition, we review the original, proof-of-concept aptamer-siRNA delivery studies and discuss recent advances in aptamer-siRNA conjugate designs for applications ranging from cancer therapy to the development of targeted antivirals. Challenges and prospects of aptamer-targeted siRNA drugs for clinical development are further highlighted.
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An Update on Aptamer-Based Multiplex System Approaches for the Detection of Common Foodborne Pathogens. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0814-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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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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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Elle IC, Karlsen KK, Terp MG, Larsen N, Nielsen R, Derbyshire N, Mandrup S, Ditzel HJ, Wengel J. Selection of LNA-containing DNA aptamers against recombinant human CD73. MOLECULAR BIOSYSTEMS 2016; 11:1260-70. [PMID: 25720604 DOI: 10.1039/c5mb00045a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LNA-containing DNA aptamers against CD73 (human ecto-5'-nucleotidase), a protein frequently overexpressed in solid tumours, were isolated by SELEX. A pre-defined stem-loop library, containing LNA in the forward primer region, was enriched with CD73 binding sequences through six rounds of SELEX with recombinant his-tagged CD73 immobilised on anti-his plates. Enriched pools isolated from rounds one, three and six were subjected to next-generation sequencing and analysed for enrichment using custom bioinformatics software. The software identified aptamer sequences via the primers and then performed several steps including sequence unification, clustering and alignment to identify enriched sequences. Three enriched sequences were synthesised for further analysis, two of which showed sequence similarities. These sequences exhibited binding to the recombinant CD73 with KD values of 10 nM and 3.5 nM when tested by surface plasmon resonance. Truncated variants of these aptamers and variants where the LNA nucleotides were substituted for the DNA equivalent also exhibited affinity for the recombinant CD73 in the low nanomolar range. In enzyme inhibition assays with recombinant CD73 the aptamer sequences were able to decrease the activity of the protein. However, the aptamers exhibited no binding to cellular CD73 by flow cytometry analysis likely since the epitope recognised by the aptamer was not available for binding on the cellular protein.
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Affiliation(s)
- Ida C Elle
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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Spiga FM, Maietta P, Guiducci C. More DNA-Aptamers for Small Drugs: A Capture-SELEX Coupled with Surface Plasmon Resonance and High-Throughput Sequencing. ACS COMBINATORIAL SCIENCE 2015; 17:326-33. [PMID: 25875077 DOI: 10.1021/acscombsci.5b00023] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
To address limitations in the production of DNA aptamers against small molecules, we introduce a DNA-based capture-SELEX (systematic evolution of ligands by exponential enrichment) protocol with long and continuous randomized library for more flexibility, coupled with in-stream direct-specificity monitoring via SPR and high throughput sequencing (HTS). Applying this capture-SELEX on tobramycin shows that target-specificity arises at cycle number 8, which is confirmed by sequence convergence in HTS analysis. Interestingly, HTS also shows that the most enriched sequences are already visible after only two capture-SELEX cycles. The best aptamers displayed K(D) of approximately 200 nM, similar to RNA and DNA-based aptamers previously selected for tobramycin. The lowest concentration of tobramycin detected on label-free SPR experiments with the selected aptamers is 20-fold smaller than the clinical range limit, demonstrating suitability for small-drug biosensing.
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Affiliation(s)
- Fabio M. Spiga
- Institute of Bioengineering, Ecole Polytechnique Féderale De Lausanne (EPFL), Lausanne, Vaud, 1015, Switzerland
| | - Paolo Maietta
- Structural Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Carlotta Guiducci
- Institute of Bioengineering, Ecole Polytechnique Féderale De Lausanne (EPFL), Lausanne, Vaud, 1015, Switzerland
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Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM. Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. Nucleic Acids Res 2015; 43:5699-707. [PMID: 25870409 PMCID: PMC4499121 DOI: 10.1093/nar/gkv308] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut—a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the ‘parent’ sequence and AptaCluster—an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods.
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Affiliation(s)
- Jan Hoinka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Alexey Berezhnoy
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Phuong Dao
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Eli Gilboa
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Teresa M Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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