Yizhou Li; Gunther Zimmermann; Jörg Scheuermann; Dario Neri
ChemBioChem, 2017, 18(9), 848-852
https://doi.org/10.1002/cbic.201600626

Abstract

Performance perfection: We used a quantitative PCR methodology to rapidly characterize DNA‐encoded chemical library selections. This approach facilitates determination of optimal experimental conditions for the recovery of binding molecules from large combinatorial libraries. Information derived from this method complements that derived from high‐throughput sequencing of libraries, before and after selection.
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.