title: Quantitative PCR is a Valuable Tool to Monitor the Performance of DNA-Encoded Chemical Library Selections.
abstract: Phage-display libraries and DNA-encoded chemical libraries (DECLs) represent useful tools for the isolation of specific binding molecules from large combinatorial sets of compounds. With both methods, specific binders are recovered at the end of affinity capture procedures by using target proteins of interest immobilized on a solid support. However, although the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DECL selections. In this article, we describe the potential and limitations of quantitative PCR (qPCR) methods for the evaluation of selection efficiency by using a combinatorial chemical library with more than 35 million compounds. In the experimental conditions chosen for the selections, a quantification of DNA input/recovery over five orders of magnitude could be performed, revealing a successful enrichment of abundant binders, which could be confirmed by DNA sequencing. qPCR provided rapid information about the performance of selections, thus facilitating the optimization of experimental conditions.
authors.affiliation: Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, 093, Zürich, Switzerland.
authors.forename: Yizhou
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, 093, Zürich, Switzerland.
authors.forename: Gunther
authors.initials: G
authors.lastname: Zimmermann
authors.affiliation: Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, 093, Zürich, Switzerland.
authors.forename: Jörg
authors.initials: J
authors.lastname: Scheuermann
authors.affiliation: Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, 093, Zürich, Switzerland.
authors.forename: Dario
authors.initials: D
authors.lastname: Neri
mesh_terms: D000071231:Carbonic Anhydrase IX / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019151:Peptide Library; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012709:Serum Albumin / Q000737:chemistry / Q000378:metabolism; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000378:metabolism
chemical_list: D019151:Peptide Library; D012709:Serum Albumin; D054852:Small Molecule Libraries; D004247:DNA; D000071231:Carbonic Anhydrase IX
keywords: DNA-encoded chemical libraries; high-throughput screening; qPCR; quantification