July 9, 2015

Genome Compiler Platform Integrates SnapFast™ DNA Cloning System

Omri Amirav-Drory, Genome Compiler
Genome Compiler CEO Omri Amirav-Drory speaking at SynBioBeta London 2015.

Genome Compiler recently announced a collaboration with Sigma-Aldrich to integrate a new vector collection, known as SnapFast™, into its software platform for DNA design and assembly. The SnapFast™ cloning technology, developed by Oxford Genetics and distributed by Sigma-Aldrich, is a flexible and versatile DNA plasmid system for creating multiple gene expression systems.
Genome Compiler offers free computer-aided design (CAD) software for genetic engineering in a drag and drop platform shown below. CAD software for molecular cloning and genetic engineering is a useful tool for synthetic biologists, as it helps manage the complexity of genetic circuit design and aids in collaborative efforts. CAD has long been a necessary element of other engineering disciplines, and Genome Compiler marks the increasing demand for such tool in synthetic biology.

The purpose of Genome Compiler is to offer an “all in one” platform for molecular cloning and genetic engineering, from designing vectors to ordering parts and primers. Users can select biological parts from the built-in library or create their own, simulate cloning reactions like Gibson Assembly, import and share data, as well as order DNA parts directly from supported suppliers such as DNA 2.0. The addition of the SnapFast™ vectors to the Genome Compiler library further increases the power of the software.

Screenshot of Genome Compiler.

Screenshot of Genome Compiler.

Streamlined Cloning with SnapFast™

Researchers use molecular cloning techniques to construct circular plasmids, which can be used to directly express a gene(s) of interest, or to insert a gene cassette directly into an organism’s genome. While this is a fundamental tool in molecular biology, genetics and modern synthetic biology, molecular cloning remains a frustrating bottleneck for research.  Plasmid construction involves obtaining a piece of DNA, modifying it with enzymes, then joining it to other pieces of DNA. It’s a laborious process that can be complex, time-consuming, and expensive, depending on the desired plasmid.

Ryan Cawood, CEO of Oxford Genetics, was inspired to resolve some of the major problems with cloning, particularly conflicting restriction sites and incompatibility between different biological systems. Construction of complex DNA expression vectors should be an easy, efficient and less expensive process. The SnapFast™ technology is based on interchangeable pieces of DNA that can be easily swapped, so the researcher doesn’t have to start the molecular cloning process from scratch.

The SnapFast™ system standardizes restriction enzyme cloning by combining their custom SnapFast™ Vector core backbone with an arrangement of DNA parts in a way that allows each component of the vector to be easily swapped in or out using restriction enzymes, as shown below. A large collection of parts is available, including 26 peptide tags, 9 reporter genes, more than 40 promoters and 10 selectable markers. This enables the synthetic biologist to control many important aspects of their genetic circuit by simply swapping components between different vectors.

The SnapFast™ concept. Source: Oxford Genetics.

The SnapFast™ concept. Source: Oxford Genetics.

Genome Compiler is Expanding the Space for Design

By linking to the SnapFast™ Vector Collection, the Genome Compiler enriches their platform with over 1650 expression plasmids for mammalian, bacterial and yeast protein production. The intellectual property free plasmids contain a wide range of frequently used DNA components and are compatible with most popular cloning methods (e.g. restriction site cloning, Gibson, LIC, SLIC, and InFusion).

“At Genome Compiler, we empower users with an intuitive and comprehensive software platform. With the new Sigma-Aldrich collaboration, we are closing the loop between research, design and information sharing”, said Omri Amirav-Drory, CEO, Genome Compiler.

Tonya Jackson, Global Product Manager at Sigma-Aldrich speaking at SynBioBeta London 2015.

Tonya Jackson, Global Product Manager at Sigma-Aldrich speaking at SynBioBeta London 2015.

“At Sigma-Aldrich, we aim to work with others to improve the researcher experience. We are happy to offer the SnapFast™ vector collection engineered by Oxford Genetics, embedded in Genome Compiler’s intuitive design tools, with easy ordering on Sigma’s premiere e-commerce platform”, said Tonya Jackson, Global Product Manager, Sigma-Aldrich.

This development further expands the capabilities of the Genome Compiler platform, which recently integrated the Addgene repository of 40,000 plasmids into its platform. Furthermore, Genome Compiler has collaborations with DNA2.0 and recently with Amyris which now offers its automated lab services for design parts through the CAD tool.

Indeed, the recent addition of the SnapFast™ system to Genome Compiler moves the software even further in the direction of an “all in one” solution for designing and ordering synthetic circuits. It is another step in the direction of offering CAD tools that are similar in capability to those in other engineering disciplines, and allow synthetic biologists to focus much more on what to build and not how to build it.

Edited by Conor McClune. Please leave your comments or questions below.