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Diffinity Genomics Using Pair of NIH Grants to Develop New Nucleic Acid Purification Products

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Diffinity Genomics said this week that it has been awarded a pair of grants worth more than $200,000 from the National Human Genome Research Institute to further develop rapid nucleic acid purification methods.

Rochester, NY-based Diffinity said that the grants will support the development of products to increase the efficiency of DNA purification for analysis with high-throughput systems such as DNA microarrays and next-generation sequencing.

Lewis Rothberg, a professor of chemistry at the University of Rochester and chief technology officer at Diffinity, is principal investigator on both grants, which begin on Sept. 1.

Rothberg's lab has developed novel materials that enable the kind of fast, inexpensive, and simple biomolecular separations needed to purify nucleic acids, according to Diffinity.

The company has a license to these technologies from the University of Rochester, and uses the materials in its flagship product, the Diffinity RapidTip for PCR purification, which the company launched in the US in June 2010 (PCR Insider, 6/17/10) after receiving more than $700,000 in grants from the National Institutes of Health to assist with the product's development (PCR Insider, 1/7/2010).

Both new projects will attempt to adapt the materials technology developed in Rothberg's lab for newer and more specific applications.

The first grant, worth a little over $104,000, will support the development of purification methods following enzyme-catalyzed nucleic acid synthesis methods, which are widely used in healthcare applications such as diagnosis, pathogen detection, and cloning for therapeutic purposes, Diffinity wrote in the grant abstract.

According to the company, a significant amount of time, money, and labor is currently spent purifying desired components of enzyme-catalyzed nucleic acid reactions while discarding elements that can interfere with further use of the DNA.

"Improving workflow and enabling automation in the cleanup steps during library generation for next-generation sequencing would remove one of the bottlenecks in that … technology for genomic mapping," according to the grant's abstract.

Current approaches to purifying these reactions require multiple steps and use reagents to bind biomolecules in solution to a substrate and then selectively re-dissolve the desired component, the company said.

Diffinity's method, on the other hand, will use silica particle surfaces that attract undesired components of a solution while leaving the desired ones in solution. This will allow the company to develop special pipette tips containing the aforementioned surfaces and enabling extraction of undesired components following enzymatic reactions in approximately one minute, Diffinity said.

Under the second grant, worth just shy of $102,000, Diffinity will attempt to adapt the DiffinityTip technology to selectively capture DNA from dissolved electrophoretic gel slices using silica particles functionalized with DNA intercalators.

Extraction of DNA from gels following electrophoresis is widely used to obtain purified size-selected DNA fragments from mixtures for downstream cloning and sequencing applications, the company explained in its grant abstract.

Current approaches to extracting DNA from gels require multiple steps taking more than 10 minutes and using several reagents, the company said. Diffinity's approach will use the same core silica surfaces to selectively adsorb or repel desired solution components in a three-step pipette-based protocol that takes less than three minutes, it added.

Diffinity's approach "is easily automated with liquid handlers for high-throughput applications," the company said. If the company is successful in Phase I of this project, it will "integrate the silica particles into pipette tips designed to enable rapid mixing; verify the efficacy for applications to DNA sequencing and cloning; and exploit the manufacturing technology developed for [RapidTip] to launch a gel-extraction product."

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