Design and Construction of a Designed Ankyrin Repeat Protein (DARPin) Display Library

Abstract Protein display systems are powerful techniques used to identify protein molecules that bind with high affinity to target proteins of interest. The initial challenge in implementing a display system is the construction of a high‐diversity naïve library. Here, we describe the methods to generate a designed ankyrin repeat protein (DARPin) display library using degenerate oligonucleotides. Specifically described is the construction of a single DARPin repeat module by overlap extension PCR, concatenation of the module by restriction enzyme digestion and ligation, and incorporation of the concatenated modules into a full‐length DARPin sequence in a bacterial cloning or display vector containing the hydrophilic N‐ and C‐terminal capping domains. Protocols for PCR amplification of DARPin sequences to estimate diversity of naïve and enriched libraries via next‐generation sequencing are included, as is a simple Linux‐based program for analysis of naïve and enriched sequences. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 : Generation of a single DARPin repeat by overlap extension PCR Basic Protocol 2 : Concatenation of DARPin repeats Basic Protocol 3 : Ligation of internal repeats into cloning/display vector containing N‐ and C‐terminal capping repeats Basic Protocol 4 : Estimation of library size and diversity by next‐generation sequencing (NGS) Basic Protocol 5 : NGS analysis of naïve and enriched libraries