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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Keywords Aptamer, Aptamer target, Database, In vitro selection, SELEX
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Journal Journal of Molecular Evolution
Note Electronic supplementary material The online version of this article (doi:10.1007/s00239-015-9708-6) contains supplementary material, which is available to authorized users.
McKeague, M. (Maureen), McConnell, E.M. (Erin M.), Cruz-Toledo, J. (Jose), Bernard, E.D. (Elyse D.), Pach, A. (Amanda), Mastronardi, E. (Emily), … DeRosa, M.C. (2015). Analysis of In Vitro Aptamer Selection Parameters. Journal of Molecular Evolution, 81(5-6), 150–161. doi:10.1007/s00239-015-9708-6