March 30, 2015

Plug and Play with DNA Constructs

antibodies
DNA constructs can be used to optimize antibodies, like those shown here that recognize the flu virus. (Image: Flickr/Day Donaldson).

DNA production is becoming cheaper than ever, propelled down a Moore’s law curve by maturing technologies and cheaper reagents. This new biosynthetic industry allows researchers to order up a customized sequence for overnight delivery.

But many users don’t just want a chain of nucleotides, they want ready-to-use sequences that can be inserted into a cell to make a product of interest. Such DNA products, known as constructs, include two components – a vector that will be read by host machinery and initiate transcription, and an inserted gene that will generate the non-native biomolecule. Constructs can be thousands of bases in length, but once they’re uploaded to the cell, production should be good to go.

This niche is where Genscript is staking its claim. “We’re the world’s largest provider for construct based gene synthesis,” says Jeffrey Hung, a Genscript Vice President, “and a lot of our growth is coming from higher demand for biologics,” or medicinal biomolecules generated through a microbial host (as opposed to an exclusively chemical synthetic process). Most frequently, the company takes orders for non-native products to be expressed in a different organism, turning the unwitting target cell into a biofactory for recombinant proteins or antibodies. In many cases, biologics – the result of intentional expression of known biomolecules – are safer than uncharacterized but empirically promising small molecules taken from a cellular milieu. And using the cell as a production platform is an appealing prospect: organisms can tune behavior and metabolism to changing conditions, so small fluctuations in temperature or reactant concentration won’t doom a costly industrial process.

For example, in an effort to identify antibodies best suited to recognize potentially threatening pathogens, a range of recombinant antibodies can be produced in a host cell. Tracking how well the displayed pathogenic molecule is bound by different antibodies can identify promising new treatment options. “And once that lead is found,” explains Hung, “we can improve upon it by making the affinity better and better,” through iterative design modifications. This sort of approach is becoming increasingly prevalent in immunological fields, including immuno-oncology and autoimmune disease research.

Genscript has also contributed to a platform for yeast genetics that can quickly narrow the search for case-specific essential genetic components. It’s called SC 2.0, and it starts by creating mutations in each of the organism’s 6,000 genes. The resulting mutants are grown in isolated wells and monitored for growth. If nothing happens, then you’ve mutated an essential gene; if the media turns cloudy with cells, then you’ve identified a non-essential component. “We can ask the simple question,” says Hung, “of which genes are specifically more important for responding to certain environments given certain environmental stimuli.” This way, experimenters can separate housekeeping genes from those needed for higher temperature growth, or increased biofuel production. Understanding which aspects of the wild type yeast lifestyle are superfluous under industrial settings highlights opportunities to trim the fat and ensure that the biologically mediated process you’re after is as efficient as possible.

“Researchers have found that about 20% of the yeast genome is essential,” says Hung, “and that 80% is where a lot of future discoveries remain to be found.”

*This article is part of a special series on DNA synthesis that also appears on Wired.com