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Diffinity Genomics Wins Two NIH Grants to Further Develop DNA Purification Tech

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Diffinity Genomics this month won a pair of grants worth a total of $700,000 from the National Institutes of Health to support the company's ongoing development of new technologies and products for rapid nucleic acid purification using specialized pipette tips.

Under the first grant, a Phase II Small Business Technology Transfer award worth $600,000 in its first year, Rochester, NY-based Diffinity will continue developing rapid methods for purifying DNA following enzyme-catalyzed nucleic acid reactions, such as those carried out in a variety of diagnostic, pathogen-detection, and cloning applications.

Meantime, Diffinity will use the second award, a Phase I STTR grant worth $100,000 over the next year, to develop pipette tip technology to rapidly remove intercalating dyes from size-selected DNA fragments isolated from electrophoretic gels prior to downstream analysis methods, including next-generation sequencing, the company said.

The NIH"s National Human Genome Research Institute is administering both grants, on which Lewis Rothberg, a professor of chemistry at the University of Rochester and chief technology officer at Diffinity, is principal investigator.

Rothberg's lab has developed technology that includes specially configured surfaces that attract undesired components of a solution while leaving the desired ones in solution. Diffinity functionalizes these surfaces in pipette tips, thus reducing the nucleic acid purification process to aspirating the reaction solution and dispensing the purified DNA reaction solution using standard laboratory pipettors.

Diffinity has a license to these technologies from the University of Rochester, and uses them its flagship product, the Diffinity RapidTip for PCR purification, which it launched in the US in June 2010 after receiving more than $700,000 in grants from the National Institutes of Health to assist with the product's development.

In addition, in May Diffinity launched the RapidTip2 for PCR purification with polymerase removal, which enables PCR purification in one minute with a single mixing step using a standard pipettor.

Diffinity's latest STTR grants are intended to help the company further develop its RapidTip technology for other, more specialized sample-prep applications, Rothberg told PCR Insider this week.

The Phase II STTR, a continuation of an STTR-funded project that Diffinity began last summer (PCR Insider, 8/22/2011), will focus primarily on rapid, efficient purification of DNA after PCR and prior to downstream applications and analysis methods.

"This grant is for enzymatic cleanup, so that means a spectrum of things, [such as] cloning, where you'd need to remove restriction enzymes before you do ligation, so they don't keep cutting," Rothberg said. "It's essentially a grant to expand the number of enzymes that we guarantee work, to do beta testing, and to validate the product for downstream applications like cloning to show that your cloning efficacy is good."

Most current approaches to purifying these reactions require multiple steps and use reagents to bind all of the biomolecules in solution to a substrate and then selectively redissolve the desired component, Diffinity noted in its grant abstract. The company proposes that its RapidTip-based end product will be able to do this in less than a minute in a single step.

At the onset, Diffinity is aiming to enable downstream applications and analysis methods other than sequencing. However, "to some degree this ought to apply to the kinds of enzymatic reactions that people do in next-generation sequencing, as well," Rothberg said. "We believe that there might be good applications there, because you're doing a lot of enzymatic reactions in those protocols, but that's not specifically what it's designed for. This wouldn't preclude, for example, a distinct other grant that … addresses that need. Because they're not identical requirements."

Under its new Phase I STTR grant, Diffinity hopes to alleviate the labor-intensiveness involved with extracting DNA from gels following electrophoresis to obtain size-selected DNA fragments as part of library preparation for NGS and other downstream applications.

"There are applications where you would like to remove intercalators from gel-extracted DNA," Rothberg said. "If you cut out a gel band, and you recover the DNA, with some products you're also recovering your ethidium bromide or acridine orange … and this product would allow you to [eliminate] that in about 30 seconds."

Rothberg noted that some existing commercial gel extraction products already perform this task, "but there are some that don't, and we're thinking we're going to augment those."

More specifically, Rothberg and colleagues hope to develop particles with surfaces that selectively bind these intercalating dyes, and to make the particles easily dispersible in water to facilitate rapid mixing and collection of impurities. The researchers also plan to ascertain whether size-selected DNA obtained with various platforms and Diffinity purification is suitable for NGS library preparation.

Diffinity in June closed a Series B financing round worth an undisclosed amount and intended to support an increase in manufacturing capacity, commercialization of new products, and expansion of its sales team (PCR Insider, 6/7/2012).

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