UC Berkeley

Genetic engineering remains a difficult task and the design, build, test cycle may take months or years to complete. Currently, all three aspects are laborious, expensive, and mostly handle volumes of tens of units. The typical process of reaching a proof of concept genetic prototype involves an intensive survey of literature, synthesizing or acquiring genes, and testing their function. Here I outline tools to address bottlenecks in the genetic engineering workflow. First, I describe the Engineered DNA Sequence Syntax Inspector (EDSSI). This software pipeline checks protein-coding DNAs for syntax errors, which are incorrect or missing elements in the DNA. By using EDSSI, researchers are able to avoid the simple but costly mistakes of point errors, misannotated gene structure, or unintended extraneous ORFs. Second, I describe Multiplex Ortholog Library Synthesis and Expression Testing (MOLSET), a method to build genes and test their expression in E. coli. MOLSET enables the multiplex synthesis and expression testing of up to a hundred genes directly from a microarray oligo pool. data generated by MOLSET is incorporated into a design synthesis algorithm called Act Synthesizer that employs this information to improve predictions of pathways. Finally, we show the usefulness of the Act synthesizer by designing and testing a pathway for product of the household painkiller, acetaminophen, in E. coli.