A guide to Direct Pathway Cloning (DiPaC) for natural product discovery

Natural products (NPs) are a major source of chemical diversity and bioactive molecules. Advances in genome sequencing and bioinformatic analysis have facilitated identification of biosynthetic gene clusters (BGCs) across diverse microorganisms and environments; however, experimental access to these pathways is often hindered by absence of genetic tools, limited availability of DNA, and complex genetic architectures. Direct Pathway Cloning (DiPaC) has emerged as an efficient and flexible synthetic biology approach to address these challenges. DiPaC combines long-amplicon PCR with in vitro DNA assembly, allowing simultaneous cloning and refactoring of biosynthetic pathways without the need for intermediate library construction, extensive in vivo recombination, or multiple antibiotic selection markers. The method provides broad flexibility in vector choice, host selection, and pathway architecture, facilitating promoter exchange, removal of inhibitory regulatory elements, and modular pathway reconstruction. This review highlights representative DiPaC applications spanning multiple NP classes and illustrates its utility in orphan BGC activation, probing biosynthetic logic, and combinatorial biosynthesis. In addition, we provide guidance on BGC selection, amplification of challenging sequences, and assembly strategies, addressing common technical obstacles. Future directions are discussed, positioning DiPaC as a cornerstone tool for modern NP research.