title: By-product formation in repetitive PCR amplification of DNA libraries during SELEX.
abstract: The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.
authors.affiliation: LIMES Institute, University of Bonn, Bonn, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Tolle
authors.affiliation: LIMES Institute, University of Bonn, Bonn, Germany.
authors.forename: Julian
authors.initials: J
authors.lastname: Wilke
authors.affiliation: Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
authors.affiliation: LIMES Institute, University of Bonn, Bonn, Germany.
authors.forename: Günter
authors.initials: G
authors.lastname: Mayer
mesh_terms: D052157:Aptamers, Nucleotide; D015723:Gene Library; D008962:Models, Theoretical; D016133:Polymerase Chain Reaction; D052156:SELEX Aptamer Technique
chemical_list: D052157:Aptamers, Nucleotide