Design, preparation, and selection of DNA-encoded dynamic librariesElectronic supplementary information (ESI) available: Materials and general methods, experimental details, library selection and sequencing methods and fold enrichment calculations. See DOI: 10.1039/c5sc02467f

We report a method for the preparation and selection of DNA-encoded dynamic libraries (DEDLs). The library is composed of two sets of DNA-linked small molecules that are under dynamic exchange through DNA hybridization. Addition of the protein target shifted the equilibrium, favouring the assembly of high affinity bivalent binders. Notably, we introduced a novel locking mechanism to stop the dynamic exchange and "freeze" the equilibrium, thereby enabling downstream hit isolation and decoding by PCR amplification and DNA sequencing. Our DEDL approach has circumvented the limitation of library size and realized the analysis and selection of large dynamic libraries. In addition, this method also eliminates the requirement for modified and immobilized target proteins. DNA-encoded dynamic libraries (DEDLs) are realized by dynamic DNA hybridization and a novel equilibrium-locking mechanism.