dsDAP: an efficient method for high-abundance DNA-encoded library construction in mammalian cells

DNA-encoded libraries are invaluable tools for high-throughput screening and functional genomics studies. However, constructing high-abundance libraries in mammalian cells remains challenging. Here, we present dsDNA-assembly-PCR (dsDAP), a novel Gibson-assembly-PCR strategy for creating DNA-encoded libraries, offering improved flexibility and efficiency over previous methods. We demonstrated this approach by investigating the impact of translation initiation sequences (TIS) on protein expression in HEK293T cells. Both CRISPR-Cas9 and piggyBac systems were employed for genomic integration, allowing comparison of different integration methods. Our results confirmed the importance of specific nucleotides in the TIS region, particularly the preference for adenine at the -3 position in high-expression sequences. We also explored the effects of library dilution on genotype-phenotype correlations. This Gibson-assembly-PCR strategy overcomes limitations of existing methods, such as restriction enzyme dependencies, and provides a versatile tool for constructing high-abundance libraries in mammalian cells. Our approach has broad applications in functional genomics, drug discovery, and the study of gene regulation. We developed a novel DNA-encoded library construction strategy named dsDNA-assembly-PCR (dsDAP). This dsDNA-based method utilizes Gibson assembly for library construction, eliminating the need for restriction endonucleases. As a result, the library preparation process becomes more straightforward and feasible compared to the in-vitro-ligation-PCR strategy. By stably integrating the dsDAP library into the HEK293T cell genome through the CRISPR-Cas9 and piggyBac systems, we investigated the impact of translation initiation sequences (TISs) on translation efficiency.