Fully Automated Enzymatic Approach to Gene Manufacturing with Seamlessly Integrated Oligonucleotide Synthesis and Assembly Stages

In response to the growing need for a fast, reliable method for de novo production of long DNA molecules on demand, Triton Systems, Inc., in collaboration of Raytheon BBN Technologies, will develop a device and process for integrated DNA oligonucleotide synthesis and gene assembly that is time- and resource-efficient, high-fidelity, easily scalable, and fully automatable.  Our device will perform the oligonucleotide synthesis process on high-capacity microarray slides, and the assembly of oligonucleotides will take place in situ in a pairwise manner for each cycle.  Our process is unique despite consisting only of standard molecular biology techniques for all operations in both synthesis and assembly stages. For our Phase I work, we will build the device and then optimize these standard molecular biology protocols to work effectively with surface-bound DNA strands and smaller volumes.  Although our method contains steps to prevent DNA molecules that were not successfully lengthened in a given synthesis or assembly cycles from interfering with downstream steps, we will implement an additional proofreading mechanism before the final amplification of our manufactured gene sequences that will prevent error-containing sequences from being amplified.  We will also devise a motif-finding algorithm that can be used in later Phases to pre-construct portions of genes that are known to occur frequently in sets of sequences relevant to DARPA’s interests