Long DNA Assembly on Electronic Nanochannel Chip Devices

The long-term objective of this research program is to greatly increase the availability of large DNA constructs for biomedical researchers, by providing a new, highly automated, and low-cost way of making long synthetic DNA molecules. Gene-length DNA is routinely used by genetic engineers to deliver narrow functionalities into engineered cells. Long DNA—which may comprise 10’s, 100’s or even 1000’s of genes—can deliver far more complex functionality into cells, such as installing entire chemical synthetic pathways into bacteria to produce valuable drugs, or delivering larger recognition and killing payloads into immune cells being programmed to target cancer cells, or having far more viruses and strains represented in mRNA vaccines, which are normally single gene-based. For optimal scaling and economics, these future long DNA assembly chips would be the same type of chip that are mass produced for processors, memory, imaging, and communications, so-called “CMOS chips”. The scaling properties of such chips have been transformative for the industries they touch and can do the same for production of designer long DNA. CMOS chip devices offer the greatest potential for miniaturization, precision automation, and low-cost deployment, far beyond what is possible with the robotic automation that is currently used in industrial biofoundries that make custom DNA. The specific approach that enables the construction of long DNA in a way that will map ideally onto future electronic CMOS chips is to use all-electronic control of DNA motion within nanoscale channels, to route around and join the small building block pieces of DNA. Towards this goal, one Aim of this project is to develop precision motion control for DNA fragments moving in the channels. The other Aim is to use this motion control to bring together and join distinct DNA fragments. The methods of this project will consist of fabricating discrete electronic nanochannel devices and using these to explore all relevant motion control parameters. Issues of biocompatibility and biofouling of will also be considered, in the context supporting the desired DNA assembly workflow. The findings from this project will directly enable the next phase to fabricate a CMOS chip device, towards the ultimate goal of dramatically increasing access to long DNA for more powerful genetic engineering in biomedical applications.