title: Analysis of In Vitro Aptamer Selection Parameters.
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.
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Maureen
authors.initials: M
authors.lastname: McKeague
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Erin M
authors.initials: EM
authors.lastname: McConnell
authors.affiliation: Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Jose
authors.initials: J
authors.lastname: Cruz-Toledo
authors.affiliation: Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada.
authors.forename: Elyse D
authors.initials: ED
authors.lastname: Bernard
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Amanda
authors.initials: A
authors.lastname: Pach
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Emily
authors.initials: E
authors.lastname: Mastronardi
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Xueru
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Beking
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Tariq
authors.initials: T
authors.lastname: Francis
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Amanda
authors.initials: A
authors.lastname: Giamberardino
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Ashley
authors.initials: A
authors.lastname: Cabecinha
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
authors.forename: Annamaria
authors.initials: A
authors.lastname: Ruscito
authors.affiliation: Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada.
authors.forename: Rocio
authors.initials: R
authors.lastname: Aranda-Rodriguez
authors.affiliation: Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. michel.dumontier@stanford.edu.|Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA. michel.dumontier@stanford.edu.
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.affiliation: Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. maria.derosa@carleton.ca.
authors.forename: Maria C
authors.initials: MC
authors.lastname: DeRosa
mesh_terms: D052157:Aptamers, Nucleotide; D052156:SELEX Aptamer Technique / Q000379:methods*
chemical_list: D052157:Aptamers, Nucleotide
keywords: Aptamer; Aptamer target; Database; In vitro selection; SELEX