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Meyer C, Berg K, Eydeler-Haeder K, Lorenzen I, Grötzinger J, Rose-John S, Hahn U. Stabilized Interleukin-6 receptor binding RNA aptamers. RNA Biol 2013; 11:57-65. [PMID: 24440854 DOI: 10.4161/rna.27447] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Interleukin-6 (IL-6) is a multifunctional cytokine that is involved in the progression of various inflammatory diseases, such as rheumatoid arthritis and certain cancers; for example, multiple myeloma or hepatocellular carcinoma. To interfere with IL-6-dependent diseases, targeting IL-6 receptor (IL-6R)-presenting tumor cells using aptamers might be a valuable strategy to broaden established IL-6- or IL-6R-directed treatment regimens. Recently, we reported on the in vitro selection of RNA aptamers binding to the human IL-6 receptor (IL-6R) with nanomolar affinity. One aptamer, namely AIR-3A, was 19 nt in size and able to deliver bulky cargos into IL-6R-presenting cells. As AIR-3A is a natural RNA molecule, its use for in vivo applications might be limited due to its susceptibility to ubiquitous ribonucleases. Aiming at more robust RNA aptamers targeting IL-6R, we now report on the generation of stabilized RNA aptamers for potential in vivo applications. The new 2'-F-modified RNA aptamers bind to IL-6R via its extracellular portion with low nanomolar affinity comparable to the previously identified unmodified counterpart. Aptamers do not interfere with the IL-6 receptor complex formation. The work described here represents one further step to potentially apply stabilized IL-6R-binding RNA aptamers in IL-6R-connected diseases, like multiple myeloma and hepatocellular carcinoma.
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Affiliation(s)
- Cindy Meyer
- Laboratory of RNA Molecular Biology; Howard Hughes Medical Institute; The Rockefeller University; New York, NY USA
| | - Katharina Berg
- Institute of Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Katja Eydeler-Haeder
- Institute of Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Inken Lorenzen
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Stefan Rose-John
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Ulrich Hahn
- Institute of Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
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Banerjee J, Nilsen-Hamilton M. Aptamers: multifunctional molecules for biomedical research. J Mol Med (Berl) 2013; 91:1333-42. [PMID: 24045702 DOI: 10.1007/s00109-013-1085-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/14/2013] [Accepted: 09/04/2013] [Indexed: 12/28/2022]
Abstract
Aptamers are single-stranded oligonucleotides that fold into well-defined three-dimensional shapes, allowing them to bind their targets with high affinity and specificity. They can be generated through an in vitro process called "Systemic Evolution of Ligands by Exponential Enrichment" and applied for specific detection, inhibition, and characterization of various targets like small organic and inorganic molecules, proteins, and whole cells. Aptamers have also been called chemical antibodies because of their synthetic origin and their similar modes of action to antibodies. They exhibit significant advantages over antibodies in terms of their small size, synthetic accessibility, and ability to be chemically modified and thus endowed with new properties. The first generation of aptamer drug "Macugen" was available for public use within 25 years of the discovery of aptamers. With others in the pipeline for clinical trials, this emerging field of medical biotechnology is raising significant interest. However, aptamers pose different problems for their development than for antibodies that need to be addressed to achieve practical applications. It is likely that current developments in aptamer engineering will be the basis for the evolution of improved future bioanalytical and biomedical applications. The present review discusses the development of aptamers for therapeutics, drug delivery, target validation and imaging, and reviews some of the challenges to fully realizing the promise of aptamers in biomedical applications.
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Affiliation(s)
- Jayeeta Banerjee
- Biology Department, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune, 411008, India,
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Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA. Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents. PLoS One 2013; 8:e71798. [PMID: 23967247 PMCID: PMC3742456 DOI: 10.1371/journal.pone.0071798] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022] Open
Abstract
Background DNA aptamers generated by cell-SELEX offer an attractive alternative to antibodies, but generating aptamers to specific, known membrane protein targets has proven challenging, and has severely limited the use of aptamers as affinity reagents for cell identification and purification. Methodology We modified the BJAB lymphoblastoma cell line to over-express the murine c-kit cell surface receptor. After six rounds of cell-SELEX, high-throughput sequencing and bioinformatics analysis, we identified aptamers that bound BJAB cells expressing c-kit but not wild-type BJAB controls. One of these aptamers also recognizes c-kit endogenously expressed by a mast cell line or hematopoietic progenitor cells, and specifically blocks binding of the c-kit ligand stem cell factor (SCF). This aptamer enables better separation by fluorescence-activated cell sorting (FACS) of c-kit+ hematopoietic progenitor cells from mixed bone marrow populations than a commercially available antibody, suggesting that this approach may be broadly useful for rapid isolation of affinity reagents suitable for purification of other specific cell types. Conclusions/Significance Here we describe a novel procedure for the efficient generation of DNA aptamers that bind to specific cell membrane proteins and can be used as high affinity reagents. We have named the procedure STACS (Specific TArget Cell-SELEX).
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Affiliation(s)
- Susanne Meyer
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - John P. Maufort
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Jeff Nie
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Brian E. McIntosh
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Lisa R. Conti
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Kareem M. Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - H. Tom Soh
- Department of Materials, University of California Santa Barbara, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - James A. Thomson
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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Taghdisi SM, Danesh NM, Sarreshtehdar Emrani A, Tabrizian K, Zandkarimi M, Ramezani M, Abnous K. Targeted delivery of Epirubicin to cancer cells by PEGylated A10 aptamer. J Drug Target 2013; 21:739-44. [PMID: 23815443 DOI: 10.3109/1061186x.2013.812095] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Clinical administrations of anthracyclines are limited by cardiotoxicity and myelosuppression. Targeted delivery of anticancer agents is especially important in reducing their side effects. In this work, A10 (Apt), an aptamer for prostate-specific membrane anytigen (PSMA), was applied for targeted delivery of Epirubicin (Epi) to LNCaP cells (PSMA(+)). Flow cytometry analysis showed that PEG-Apt-Epi complex was internalized effectively to LNCaP cells (PSMA(+)), but not to PC3 cells (PSMA(-)). This fact was confirmed by less cytotoxicity of PEG-Apt-Epi complex in PC3 cells in comparison with Epi alone. No significant change in viability between Epi- and complex-treated LNCaP cells was observed. In conclusion, PEG-Apt-Epi complex is an efficient and simple system for specific delivery of drug to PSMA-expressing cell lines.
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Affiliation(s)
- Seyed Mohammad Taghdisi
- Department of Pharmaceutical Biotechnology, Zabol University of Medical Sciences, Zabol, Iran
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55
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Selection of DNA aptamers for capture and detection of Salmonella Typhimurium using a whole-cell SELEX approach in conjunction with cell sorting. Appl Microbiol Biotechnol 2013; 97:3677-86. [PMID: 23494620 DOI: 10.1007/s00253-013-4766-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/04/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Alternative ligands such as nucleic acid aptamers can be used for pathogen capture and detection and offer advantages over antibodies, including reduced cost, ease of production and modification, and improved stability. DNA aptamers demonstrating binding specificity to Salmonella enterica serovar Typhimurium were identified by whole-cell-systematic evolution of ligands by exponential enrichment (SELEX) beginning with a combinatorial library of biotin-labeled single stranded DNA molecules. Aptamer specificity was achieved using whole-cell counter-SELEX against select non-Salmonella genera. Aptamers binding to Salmonella were sorted, cloned, sequenced, and characterized for binding efficiency. Out of 18 candidate aptamers screened, aptamer S8-7 showed relatively high binding affinity with an apparent dissociation constant (K d value) of 1.73 ± 0.54 μM and was selected for further characterization. Binding exclusivity analysis of S8-7 showed low apparent cross-reactivity with other foodborne bacteria including Escherichia coli O157: H7 and Citrobacter braakii and moderate cross-reactivity with Bacillus cereus. Aptamer S8-7 was successfully used as a ligand for magnetic capture of serially diluted Salmonella Typhimurium cells, followed by downstream detection using qPCR. The lower limit of detection of the aptamer magnetic capture-qPCR assay was 10(2)-10(3) CFU equivalents of Salmonella Typhimurium in a 290-μl sample volume. Mean capture efficiency ranged from 3.6 to 12.6 %. Unique aspects of the study included (a) the use of SELEX targeting whole cells; (b) the application of flow cytometry for aptamer pool selection, thereby favoring purification of ligands with both high binding affinity and targeting abundant cell surface moieties; and (c) the use of pre-labeled primers that circumvented the need for post-selection ligand labeling. Taken together, this study provides proof-of-concept that biotinylated aptamers selected by whole-cell SELEX can be used in a qPCR-based capture-detection platform for Salmonella Typhimurium.
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Tolle F, Mayer G. Dressed for success – applying chemistry to modulate aptamer functionality. Chem Sci 2013. [DOI: 10.1039/c2sc21510a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Thiel WH, Bair T, Peek AS, Liu X, Dassie J, Stockdale KR, Behlke MA, Miller FJ, Giangrande PH. Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PLoS One 2012; 7:e43836. [PMID: 22962591 PMCID: PMC3433472 DOI: 10.1371/journal.pone.0043836] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/30/2012] [Indexed: 01/05/2023] Open
Abstract
Background The broad applicability of RNA aptamers as cell-specific delivery tools for therapeutic reagents depends on the ability to identify aptamer sequences that selectively access the cytoplasm of distinct cell types. Towards this end, we have developed a novel approach that combines a cell-based selection method (cell-internalization SELEX) with high-throughput sequencing (HTS) and bioinformatics analyses to rapidly identify cell-specific, internalization-competent RNA aptamers. Methodology/Principal Findings We demonstrate the utility of this approach by enriching for RNA aptamers capable of selective internalization into vascular smooth muscle cells (VSMCs). Several rounds of positive (VSMCs) and negative (endothelial cells; ECs) selection were performed to enrich for aptamer sequences that preferentially internalize into VSMCs. To identify candidate RNA aptamer sequences, HTS data from each round of selection were analyzed using bioinformatics methods: (1) metrics of selection enrichment; and (2) pairwise comparisons of sequence and structural similarity, termed edit and tree distance, respectively. Correlation analyses of experimentally validated aptamers or rounds revealed that the best cell-specific, internalizing aptamers are enriched as a result of the negative selection step performed against ECs. Conclusions and Significance We describe a novel approach that combines cell-internalization SELEX with HTS and bioinformatics analysis to identify cell-specific, cell-internalizing RNA aptamers. Our data highlight the importance of performing a pre-clear step against a non-target cell in order to select for cell-specific aptamers. We expect the extended use of this approach to enable the identification of aptamers to a multitude of different cell types, thereby facilitating the broad development of targeted cell therapies.
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Affiliation(s)
- William H. Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Thomas Bair
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Andrew S. Peek
- Roche Molecular Systems, San Francisco, California, United States of America
| | - Xiuying Liu
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Justin Dassie
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Katie R. Stockdale
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Francis J. Miller
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Radiation Oncology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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Zhu Q, Shibata T, Kabashima T, Kai M. Inhibition of HIV-1 protease expression in T cells owing to DNA aptamer-mediated specific delivery of siRNA. Eur J Med Chem 2012; 56:396-9. [PMID: 22907035 DOI: 10.1016/j.ejmech.2012.07.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/28/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
Abstract
Targeted delivery is a promising way to improve the safety and efficiency of siRNA delivery. We show that a DNA aptamer could be used to deliver siRNA into CD4(+) T cells specifically. The DNA aptamer was obtained from the conversion of a reported RNA aptamer that binds to CD4 protein on the surface of T cells. It was covalently conjugated to the sense strand of the siRNA targeting HIV-1 protease (HIV-PR). The resulting DNA aptamer-siRNA chimera could specifically enter into CD4(+) T cells and efficiently knock down the expression of exogenous HIV-PR gene. This study provides the first evidence that the DNA aptamer with intrinsic stability has a greater potential to be used for siRNA delivery.
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Affiliation(s)
- Qinchang Zhu
- Faculty of Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-Machi, Nagasaki 852-8521, Japan
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Binning JM, Leung DW, Amarasinghe GK. Aptamers in virology: recent advances and challenges. Front Microbiol 2012; 3:29. [PMID: 22347221 PMCID: PMC3274758 DOI: 10.3389/fmicb.2012.00029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 01/17/2012] [Indexed: 01/23/2023] Open
Abstract
Aptamers generated from randomized libraries of nucleic acids have found utility in a wide variety of fields and in the clinic. Aptamers can be used to target both intracellular and extracellular components, including small molecules, proteins, cells, and viruses. With recent technological developments in stringent selection and rapid isolation strategies, it is likely that aptamers will continue to make an impact as useful tools and reagents. Although many recently developed aptamers are intended for use as therapeutic and diagnostic agents, use of aptamers for basic research, including target validation, remains an active area with high potential to impact our understanding of molecular mechanisms and for drug discovery. In this brief review, we will discuss recent aptamer discoveries, their potential role in structural virology, as well as challenges and future prospects.
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Affiliation(s)
- Jennifer M Binning
- Department of Pathology and Immunology, Washington University School of Medicine St. Louis, MO, USA
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60
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Göringer HU. Parasite-specific aptamers as biosynthetic reagents and potential pharmaceuticals. Trends Parasitol 2012; 28:106-13. [PMID: 22300805 DOI: 10.1016/j.pt.2011.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/28/2011] [Accepted: 12/29/2011] [Indexed: 10/14/2022]
Abstract
Aptamers are short, synthetic nucleic acid molecules. They are generated by a Darwinian-type in vitro evolution method known as 'systematic evolution of ligands by exponential enrichment' (SELEX). SELEX represents an experimental platform to identify rare ligands with predetermined functionality from combinatorial nucleic acid libraries. Since its discovery about 20 years ago the method has been instrumental in identifying a large number of aptamers that recognize targets of very different chemistry and molecular complexity. Although aptamers have been converted into sophisticated biomolecular tools for a diverse set of technologies, only a limited number of aptamers have been selected as binding reagents for parasites or parasite-derived molecules. Here the published examples of aptamers that target Leishmania-, Trypanosoma- and Plasmodia-specific molecules are reviewed.
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Affiliation(s)
- H Ulrich Göringer
- Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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61
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Meyer C, Eydeler K, Magbanua E, Zivkovic T, Piganeau N, Lorenzen I, Grötzinger J, Mayer G, Rose-John S, Hahn U. Interleukin-6 receptor specific RNA aptamers for cargo delivery into target cells. RNA Biol 2012; 9:67-80. [PMID: 22258147 PMCID: PMC3342945 DOI: 10.4161/rna.9.1.18062] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aptamers represent an emerging strategy to deliver cargo molecules, including dyes, drugs, proteins or even genes, into specific target cells. Upon binding to specific cell surface receptors aptamers can be internalized, for example by macropinocytosis or receptor mediated endocytosis. Here we report the in vitro selection and characterization of RNA aptamers with high affinity (Kd = 20 nM) and specificity for the human IL-6 receptor (IL-6R). Importantly, these aptamers trigger uptake without compromising the interaction of IL-6R with its natural ligands the cytokine IL-6 and glycoprotein 130 (gp130). We further optimized the aptamers to obtain a shortened, only 19-nt RNA oligonucleotide retaining all necessary characteristics for high affinity and selective recognition of IL-6R on cell surfaces. Upon incubation with IL-6R presenting cells this aptamer was rapidly internalized. Importantly, we could use our aptamer, to deliver bulky cargos, exemplified by fluorescently labeled streptavidin, into IL-6R presenting cells, thereby setting the stage for an aptamer-mediated escort of drug molecules to diseased cell populations or tissues.
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Affiliation(s)
- Cindy Meyer
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Katja Eydeler
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Eileen Magbanua
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Tijana Zivkovic
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Nicolas Piganeau
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Inken Lorenzen
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute; University of Bonn; Bonn, Germany
| | - Stefan Rose-John
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Ulrich Hahn
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
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Advances in binder identification and characterisation: the case of oligonucleotide aptamers. N Biotechnol 2011; 29:550-4. [PMID: 22178698 DOI: 10.1016/j.nbt.2011.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 02/07/2023]
Abstract
Aptamers represent an important class of synthetic protein binders useful for proteome-wide applications. The identification and characterisation of such molecules have been greatly facilitated by the development of Systematic Evolution of Ligands by Exponential Amplification (SELEX). Since then numerous advances and alternatives to improve efficient aptamer discovery have been reported. In the present manuscript we discuss the recent advances performed around the SELEX approach that may help to expand the availability of new aptamers and the subsequent applications that may be developed.
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