Hierarchical Multiplex Pairwise Golden Gate Assembly: Converting Short Oligo-Pools into Longer DNA Libraries

Abstract

Large-scale screening and high-throughput experimental data generation are essential for advancing AI-driven biomolecular design. However, these processes are economically unfeasible due to the high costs associated with synthesizing gene-sized DNA sequences at scale. To address this challenge, we developed a novel method for the high-throughput assembly of gene-sized DNA sequences, starting from cost-effective chip-synthesized oligo-pools. In contrast to Polymerase Cycling Assembly (PCA) methods, we employed Golden Gate Assembly (GGA) to facilitate the ligation of short DNA fragments. This approach enabled us to successfully assemble high-quality DNA libraries containing up to 96 gene-sized sequences (600 bp) in a single-pot reaction, with convenient retrieval of individual sequences. If numerous reactions are conducted in parallel---for example, in a 96-well plate---we can readily assemble up to 9,216 (96 x 96)) genes. When combined with advances in automation technologies, this enables the efficient and cost-effective synthesis of gene-sized DNA sequences at scale, thereby accelerating the generation of experimental data for the biomolecular design community.