j5 DNA Assembly Design Automation Software

Abstract

Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. coli. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.

Bricks and blueprints: methods and standards for DNA assembly

“…Software tools will increasingly play an important role in DNA assembly, and are already required for the design of parts for modular DNA assembly 54,55,59 and used in the experimental planning and quality control of large and complex projects [67][68][69] . Many of these software tools can also control liquid handling robots and their ability to automate hundreds of complex modular assemblies has been recently demonstrated 62 .…”

“…By formatting parts and protocols according to a standard, future workflows will be set so that parts can be combined efficiently over sequential tiers and exchanged between projects around the world. As these standards are implemented the next logical steps for DNA assembly should recapitulate mature engineering disciplines: enabling software will be developed, automation of the labour will be introduced and ultimately the work of cloning will be commercially outsourced just as it is already done for gene synthesis and DNA sequencing.Software tools will increasingly play an important role in DNA assembly, and are already required for the design of parts for modular DNA assembly 54,55,59 and used in the experimental planning and quality control of large and complex projects [67][68][69] . Many of these software tools can also control liquid handling robots and their ability to automate hundreds of complex modular assemblies has been recently demonstrated 62 .…”

Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes

“…In particular, the booming field of synthetic biology (1) demonstrates the feasibility of de novo synthesis of viral genomes (2)(3)(4)(5), bacterial genomes (6,7), and eukaryotic chromosomes (8,9). The technologies underpinning synthetic biology are advanced DNA synthesis and assembly (10), genome editing (11,12), and computational assisted designs (13)(14)(15), which are all becoming commoditized and thus increasingly available to the public. The advance of synthetic biology promises to ultimately improve human living conditions through a better understanding of fundamental sciences as well as a multitude of practical applications.…”

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

“…In turn, by making it easier to implement novel designs, CAD tools can dramatically reduce the number of genetic variants that must be tested, which decreases the amount of large-scale, trial-and-error experimentation and laboratory infrastructure required. By employing algorithms that optimize the process of genetic construction (e.g., identifying ways to reuse genetic material, and otherwise minimize de novo oligonucleotide synthesis), new DNA design software like 'j5' (Hillson et al 2011;Chen et al 2012) further lessens the volumes and costs of materials and reagents. TeseleGen, Inc., a company developing commercial versions of the j5 DNA design software, has said that their existing design algorithms can reduce the time needed to construct a simple metabolic pathway by 20 % (to approximately 2 weeks), and at half the cost ($700 USD), compared to traditional cloning.…”