Although synthetic processes inspired by life’s chemistry are inherently messy and complex, they may yet yield to bioengineers’ attempts to impose order. For example, engineers have been reporting progress in standardizing the design and assembly of artificial DNA. Still, despite various attempts at simplifying the creation of synthetic DNA, none have been completely successful. A key limitation: the lengths of DNA constructs that can be linked together at the same time.
A recent attempt to overcome the limitations of existing approaches has been introduced by scientists at Imperial College London. They have defined a new physical standard for DNA parts called BASIC, which stands for Biopart Assembly Standard for Idempotent Cloning.
BASIC, the scientists assert, combines the best features of the most popular methods while overcoming their limitations, creating a system that is fast, flexible, and accurate. The new technique, the scientists add, should enable greater advances in research and could offer industry a way to automate the design and manufacture of synthetic DNA.
Geoff Baldwin, Ph.D., from Imperial's Department of Life Sciences, explained, “BASIC uses standardized parts which, like Lego, have the same joining device, so parts will fit together in any order.”
“Unlike some systems that can only join two parts at a time, forcing the gene to be built in several, time consuming steps, BASIC enables multiple parts to be joined together at once,” Dr. Baldwin continued. “It is also 99% accurate, compared to bespoke designs which usually have an accuracy of around 70%.”
The Imperial group presented its work March 8 in ACS Synthetic Biology, in an article entitled, “BASIC: a new Biopart Assembly Standard for Idempotent Cloning provides accurate, single-tier DNA assembly for synthetic biology.” BASIC, the article’s authors noted, exploits the principle of orthogonal linker-based DNA assembly.
“We demonstrate a new robust method for assembly, based on type IIs restriction cleavage and ligation of oligonucleotides with single stranded overhangs that determine the assembly order,” the authors wrote. “It allows for efficient, parallel assembly with great accuracy: four-part assemblies achieved 93% accuracy with single antibiotic selection and 99.7% accuracy with double antibiotic selection, while seven-part assemblies achieved 90% accuracy with double antibiotic selection.”
According to a press announcement from Imperial, BASIC is fast to use because it can draw on a large database of standardized parts, which can be produced in bulk and stored for use as required, rather than creating new parts each time. The announcement added that the standardization and accuracy of the process means that it could be used on an industrial scale.
BASIC is already set to be used in a high-throughput automated process in SynbiCITE, the innovation and knowledge centre (IKC) based at Imperial which is promoting the adoption of synthetic biology by industry. Additional industrial partners, including Isogenica, are also already making use of BASIC in their research laboratories.