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Purigen Biosystems Wins SBIR Funding to Develop Isotachophoresis Chip for Nucleic Acid Prep


Purigen Biosystems, a Bay Area biotech company founded in 2012, recently received $150,000 in Phase I Small Business Innovation Research funding from the National Institutes of Health to develop a device for nucleic acid sample prep.

The funding, administered by the National Human Genome Research Institute, will specifically help the firm develop a microfluidics-based chip which uses isotachophoresis to purify and quantify nucleic acids from different kinds of samples. The purified nucleic acid would then be immediately compatible with a wide range of downstream analyses including microarrays, enzymatic amplification, and sequencing, according to the company's SBIR grant abstract.

Purigen CTO Amy Hiddessen told PCR Insider this week that the product is expected to launch in 2015, and that Purigen has already begun placing prototypes in the hands of testers at both academic and clinical laboratories.

Hiddessen and CEO Klint Rose have experience bringing new technologies to market. They were early developers of droplet digital PCR at QuantaLife, a company acquired by BioRad in 2011 for $162 million.

Purigen's sample preparation system is based on foundational work done at Stanford University, in the laboratory of company co-founder and CSO, Juan Santiago. Hiddessen said "We're applying the research and inventions from the Santiago lab to commercialize this technology and make it available to the wider community. We have the benefit that the technology is already very robust and very well fleshed out, thanks to the depth of work coming from Santiago's lab."

Purigen's method to isolate and quantify nucleic acids exploits "a lucky break of nature," said Hiddessen, "which is that DNA and RNA, nucleic acids, have a very high electrophoretic mobility in an electric field. Compared to things like inhibitors, or even proteins, nucleic acids in an electric field will race far ahead of contaminating agents."

The device purifies, concentrates, and even quantifies low-abundance nucleic acids, said Hiddessen. The technology, she said, can produce a 1,000- to 10,000-fold concentration of the nucleic acid from a sample.

"If you only start with a few hundred cells, while the extracted DNA or RNA might begin as a more dilute and dispersed solution, our technique both purifies and concentrates it into a very tight zone. This concentration enables us to more sensitively quantify it with a fluorescence detector and determine how much material was present in the initial sample," Hiddessen said.

She emphasized that, unlike current commercially available sample prep technologies, the quantification happens "while your sample is being extracted and purified, so there is no need to sacrifice material. Everything that's quantified is delivered to the user at the end of the process."

Purigen's sample prep technique is especially efficacious, said Hiddessen, because of the unique buffer chemistries the company has developed. "It's important to note our buffers are fully compatible with downstream enzymatic assays — we selectively engineer them in a way that does not reduce compatibility but optimizes the electrophoretic efficiency," she said.

For different sample types and prep needs, she claimed Purigen has developed different optimal buffers, and will commercialize these into kits "similar to other companies … that sell kits to extract nucleic acids from cells, or tissue, or blood," she said. Hiddessen claimed that the company has already shown the device can be used on urine, blood, tissue, cell culture (bacterial and mammalian), and parasites such as malaria.

For FFPE samples, she said "we have not developed the final kit, but it's in process and will be available when we launch the system." In terms of the final commercial product, Hiddessen said, "the technology is extremely widely applicable and versatile."

The electrophoretic technique is also "surface-free," said Hiddessen, so there are no columns or binding steps that could result in loss of precious low-abundance samples. Purigen has also developed both off- and on-chip lysis, so that, for example, a small number of cells could be injected into the chip, lysed, and "then the nucleic acid is purified from all inhibitors, quantified, and delivered to the user for use," said Hiddessen.

Hiddessen also claimed the chip is able to purify nucleic acids directly from whole blood, without any pre-processing. This could be useful for cell-free DNA and microRNA. "Promising evolving biomarkers are going to benefit from better sample prep," she said. "Those kinds of customers would benefit from an instrument that Purigen would sell."

At the same time, Purigen believes its technology can help with samples like liquid biopsies or even FFPE in the clinical space, "so we're not limited to where our customers would find use of our instrument," she added.

During Phase I of the SBIR grant Purigen will target extraction from 1- to 60-microliter sample volumes in a system capable of processing four samples in parallel. Should Purigen received Phase II funding, it will then work to develop a monolithic chip capable of eight samples each with 1- to 100-microliter volumes.

Purigen hopes that its device will be used in both academic and CLIA lab environments. It has already made prototypes to put in the hands of customers, and is "collecting their feedback in order to best build what the community wants and needs. These efforts also have the beneficial effect that we educate the community on some of the limitations of sample prep with current technologies," said Hiddessen.

Hiddessen estimated the cost of Purigen's device would be competitive with current technologies but would provide an advantage because it combines the work of multiple machines. "Our instrument will offer an integrated solution for sample extraction and purification, plus in-line quantification, so our customers will see a favorable price improvement," said Hiddessen.

Hiddessen said that Purigen hopes to eventually partner with a larger company such that its device is used as the "front-end sample prep" for a diagnostic tool.

The technology, she added, could be "integrated into powerful analyses platforms for which there is already a market, but for which current solutions suffer from lack of highly sensitive, highly unbiased sample prep. This is where we see ourselves fitting in the long term."

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