Integrated Circuit Electrical DNA Assembly

Avery Bio Corporation, San Diego CA

Investigators

Abstract

PROJECT SUMMARY ABSTRACT: Current commercial DNA gene synthesis has reached a mature state in which genes still cost hundreds of dollars each to customers. Moreover, further cost reductions are fundamentally limited by the scalability limitations of the underlying production technology, which is based on industrial robotic automation. This high cost of genes greatly limits advances in synthetic biology, which requires extensive trial-based engineering to design optimal genes for diverse applications. The demand for genes to serve such optimization efforts is practically unlimited, and tens of thousands to millions of gene trials would be undertaken were it economical to do so. In addition, recent advances in AI for design create an even greater unmet demand for making many thousands to millions of genes to test trial AI designs or to generate AI training data. Procuring genes at these scales is economically unfeasible, and thus there is a great need for new gene synthesis technologies that can radically lower the costs of making many trial genes. In this Phase II development effort, we will build on Phase I results to create a system prototype for a new method for synthesizing genes in a massively parallel fashion on a scalable electronic semiconductor chip device, which has the potential to synthesize and assemble up to millions of specified gene designs. This disruptive chip technology offers the potential of up to million-fold reductions in the cost of making individual genes, removing the economic barriers to trial-based bioengineering and to maturing AI-design methods. The method and system to be developed in this project rely on the fundamental ability to independently and in parallel synthesize DNA oligos on multiple electrodes under electronic control, and to then in parallel transport and assemble these oligos under precision electronic control in order to produce desired genes, also residing on electrodes. These many genes can then be transported off chip for subsequent uses, under further electronic control. The transformative power of chip technology is such that by doing all of this on a scalable semiconductor chip device electrode array, up to one hundred million specified oligos can be produced in parallel. These oligos can be assembled into up to approximately 1 million genes, resulting in disruptive scaling advances. Methods of error correction are further included to limit gene sequence error rates. The foundational oligo synthesis chip technology has been developed previously at our company, and our prior SBIR Phase I project developed the key methods of electrically controlling oligo transport, hybridization, sequence error correction, and assembly into longer DNA segments on discrete electrodes. This present Phase II effort will optimize the gene assembly workflow and map it onto the latest generation of our proprietary oligo synthesis chip for scalable demonstrations, thereby integrating our synthesis and assembly capabilities into a prototype chip for gene assembly. Final demonstrations include the production of functional genes and entire small viral genomes.