S108: Genetic Design, Synthesis and Assembly Tools for Synthetic Biology Engineering

With the completion of a myriad genome sequencing projects, the emergence of metagenomics and significant progress in understanding and building living systems, synthetic biology engineering has expanded into many applications including the rational optimization of complex pathways, construction and characterization of genetic circuits of increasing complexity and the functional re-design of existing biological systems.  Design, construction and validation of genetic circuit, pathway and genome engineering workflows are powered by a comprehensive toolbox that includes intelligent metabolic and genetic design software, sequence verified, scaled, cost-effective gene synthesis and precise, genetic assembly and editing technologies able to address genetic constructs of various size ranges.

We present a growing set of integrated technologies that provide state-of-the-art rational genetic design and simulation, gene synthesis and seamless, simultaneous, flexible, and highly efficient assembly, editing and transfer of genetic elements designed for a wide size range (10s to 100,000s base pairs).  The paradigm of next generation deep sequencing to build a foundational understanding at the genomic and transcriptome levels enabling initial metabolic models to facilitate directed engineering will be presented.  Scaled, cost-effective gene synthesis methods, formats and process considerations will be discussed.  Tools for vector construction, higher order HTP assembly and precision editing of genetic elements in vitro and in vivo will be described.   Desk-top and web-based assembly/design software tool and resources to design and manipulate large DNA constructs in silico will be presented in the context of research and applied technologies to enhance the development of synthetic biology engineering capabilities.