A perspective and demonstration of an approach to screening synthetic nucleic acid orders containing short nucleic acid sequences

Screening of nucleic acid synthesis orders is expanding to include short, single-stranded DNA orders in efforts to ensure potentially harmful genes and genomes cannot be synthesized by illegitimate or irresponsible customers. Short sequence fragments are not as information rich as gene sequences, typically require assembly to be functional, and are much cheaper to produce than genes. Thus, here we provide the perspective that the screening of sequence fragments requires a different approach than sequence-by-sequence screening by considering the context of other fragments in the order or across orders. Additional and alternative metrics should be included while screening fragments, such as fraction of the gene/genome covered and evidence of potential use for assembly to enable efficient and accurate biosecurity screening. We further demonstrate two existing biosecurity tools, UltraQUICK and Aclid that provide outputs for better understanding the threat of orders containing fragments. This perspective provides a foundation for how short DNA fragments, including oligo pools, should be screened and leaves the reader with considerations for overall risk assessments of such orders based on the functional and taxonomic characteristics of the order.