Quantitative assessment of affinity selection performance using DNA-encoded chemical libraries.

DNA-Encoded chemical libraries are often used for the discovery of ligands against protein targets of interest. These large collections of DNA-barcoded chemical compounds are typically screened by using affinity capture methodologies followed by PCR amplification and DNA sequencing procedures. However, the performance of individual steps in the selection procedures has been scarcely investigated so far. Here, we describe a quantitative analysis of selection experiments, using three ligands with different affinity to carbonic anhydrase IX as model compounds. In a first set of experiments, we used quantitative PCR (qPCR) procedures, in order to evaluate the recovery and selectivity for affinity capture procedures performed on different solid phase supports, which are commonly used for library screening. In a second step, we used both qPCR and analysis of DNA sequencing results, in order to assess the recovery and selectivity of individual carbonic anhydrase IX ligands in a library, containing 360'000 compounds. Collectively, our study reveals that selection procedures can be efficient for ligands with submicromolar dissociation constant to the target protein of interest, but also that selection performance dramatically drops when 10^4 copies per library member are used as input.