The case for trypsin release of affinity-selected phages

Abstract

Libraries of phages displaying diverse peptides are typically surveyed by affinity selection, using immobilized biomolecules as selectors. After exposing the library to the selector and washing away unbound phages, the bound phages are enriched for clones displaying selector binding peptides. Those phages are recovered by release from the selector and propagation in fresh host cells. Release is generally achieved by weakening the peptide-selector interaction without impairing phage infectivity. A perennial concern with this mode of release is recovery bias—that is, underrepresentation of the highest-affinity peptides because they are not effectively released. Here we argue for trypsin digestion as a superior release mode. It requires that the displayed peptide be connected to the phage body through a trypsin-sensitive tether, and exploits the resistance of the phage itself to that protease. We show that trypsin release is nearly complete even when phages are captured by multiple irreversible bonds, which implies little or no recovery bias.