Analysis of In Vitro Aptamer Selection Parameters
Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics a...
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| Published in | Journal of molecular evolution Vol. 81; no. 5-6; pp. 150 - 161 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Springer US
01.12.2015
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0022-2844 1432-1432 |
| DOI | 10.1007/s00239-015-9708-6 |
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| Abstract | Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success. |
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| AbstractList | Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success. Issue Title: Special Issue on In Vitro Selection: A quarter century of finding needles in haystacks Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success. |
| Author | Bernard, Elyse D. Beking, Michael Zhang, Xueru Giamberardino, Amanda Cabecinha, Ashley Francis, Tariq Ruscito, Annamaria Mastronardi, Emily Pach, Amanda DeRosa, Maria C. McConnell, Erin M. Aranda-Rodriguez, Rocio Dumontier, Michel Cruz-Toledo, Jose McKeague, Maureen |
| Author_xml | – sequence: 1 givenname: Maureen surname: McKeague fullname: McKeague, Maureen organization: Chemistry Department, Carleton University – sequence: 2 givenname: Erin M. surname: McConnell fullname: McConnell, Erin M. organization: Chemistry Department, Carleton University – sequence: 3 givenname: Jose surname: Cruz-Toledo fullname: Cruz-Toledo, Jose organization: Biology Department, Carleton University – sequence: 4 givenname: Elyse D. surname: Bernard fullname: Bernard, Elyse D. organization: Environmental Health Science and Research Bureau, Health Canada, Tunney’s Pasture – sequence: 5 givenname: Amanda surname: Pach fullname: Pach, Amanda organization: Chemistry Department, Carleton University – sequence: 6 givenname: Emily surname: Mastronardi fullname: Mastronardi, Emily organization: Chemistry Department, Carleton University – sequence: 7 givenname: Xueru surname: Zhang fullname: Zhang, Xueru organization: Chemistry Department, Carleton University – sequence: 8 givenname: Michael surname: Beking fullname: Beking, Michael organization: Chemistry Department, Carleton University – sequence: 9 givenname: Tariq surname: Francis fullname: Francis, Tariq organization: Chemistry Department, Carleton University – sequence: 10 givenname: Amanda surname: Giamberardino fullname: Giamberardino, Amanda organization: Chemistry Department, Carleton University – sequence: 11 givenname: Ashley surname: Cabecinha fullname: Cabecinha, Ashley organization: Chemistry Department, Carleton University – sequence: 12 givenname: Annamaria surname: Ruscito fullname: Ruscito, Annamaria organization: Chemistry Department, Carleton University – sequence: 13 givenname: Rocio surname: Aranda-Rodriguez fullname: Aranda-Rodriguez, Rocio organization: Environmental Health Science and Research Bureau, Health Canada, Tunney’s Pasture – sequence: 14 givenname: Michel surname: Dumontier fullname: Dumontier, Michel email: michel.dumontier@stanford.edu organization: Biology Department, Carleton University, Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University – sequence: 15 givenname: Maria C. surname: DeRosa fullname: DeRosa, Maria C. email: maria.derosa@carleton.ca organization: Chemistry Department, Carleton University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26530075$$D View this record in MEDLINE/PubMed |
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| Snippet | Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However,... Issue Title: Special Issue on In Vitro Selection: A quarter century of finding needles in haystacks Nucleic acid aptamers are novel molecular recognition tools... |
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| SubjectTerms | Acids Animal Genetics and Genomics Aptamers, Nucleotide Biomedical and Life Sciences Cell Biology Evolutionary Biology Life Sciences Microbiology Molecular biology Nucleic acids Original Article Parameter estimation Peptides Plant Genetics and Genomics Plant Sciences SELEX Aptamer Technique - methods |
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| Title | Analysis of In Vitro Aptamer Selection Parameters |
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