Designing extensible protein-DNA interactions for synthetic biology

Protein-DNA interactions are essential to constructing biological devices for synthetic gene circuits. Ideal devices should be interoperable and extensible with respect to each other. They should also exhibit minimal unwanted interactions with the host cells in which they reside and be portable between different host chassis. Here, we discuss two classes of protein-DNA devices, memory modules and transcription factors, that can be used to construct genetic circuits with novel functionalities. In addition, we describe a methodology for identifying candidate DNA targets to be used in designing artificial protein-DNA interactions. We identified 9 base-pair (bp) sites within each of six useful host organisms that were absent in individual host genomes but were unable to find any 9 bp sites that were absent from all of the genomes. Extending our search to 12 bp and 15 bp DNA sequences revealed tens of thousands and millions, respectively, of DNA sequences that were absent in all host organisms we evaluated; these sequences were targetable by publicly accessible zinc-finger methodologies. By targeting these sites, it may be possible to build interoperable, orthogonal, and portable protein-DNA devices. This work lays a foundation for future efforts to engineer novel biological devices in the emerging field of synthetic biology.