A robust pipeline for rapid production of versatile nanobody repertoires

Nanobodies are single domain antibodies derived from the variable regions of Camelidae atypical immunoglobulins. They show great promise as high affinity reagents for research, diagnostics and therapeutics due to their high specificity, small size (~15 kDa) and straightforward bacterial expression. However, identification of repertoires with sufficiently high affinity has proven time consuming and difficult, hampering nanobody implementation. Here, we present a rapid, straightforward approach that generates large repertoires of readily expressible recombinant nanobodies with high affinities and specificities against a given antigen. We demonstrate the efficacy of this approach through the production of large repertoires of nanobodies against two antigens, GFP and mCherry, with K(d) values into the sub-nanomolar range. After mapping diverse epitopes on GFP, we were also able to design ultra-high affinity dimeric nanobodies with K(d)s down to ~30 pM. The approach presented is well-suited for the routine production of high affinity capture reagents for various biomedical applications.