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Exiqon Launches Bioinformatics Tools for miRNA, mRNA Analysis Using LNA-Based Assays

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Exiqon this week launched a pair of bioinformatics products designed to extend the capabilities of its locked nucleic acid technology for detecting and analyzing microRNAs and mRNA.

The first software product will allow users to design custom quantitative real-time PCR assays for microRNA quantification using Exiqon's miRCURY LNA microRNA PCR kits; while the second product will enable customers to design locked nucleic acid probes to detect mRNA using in situ hybridization.

The first software product, which will be available from Exiqon online for customers using the company's miRCURY LNA PCR kits, is Exiqon's first design software for microRNA applications, an increasing area of focus for the company and for researchers in general, Henrik Pfundheller, vice president of sales and marketing for Exiqon, said this week.

"There are an increasing number of microRNAs and other small RNAs being found daily by next-generation sequencing," Pfundheller said. Exiqon currently offers validated assays for many of these miRNAs and small RNAs, "but it is impossible to keep pace with a lot of the new things that come out," Pfundheller added. "So with [this] software, we are addressing this need in the market to actually get qPCR primers for newly identified miRNAs and other small RNAs."

The software works by applying a proprietary algorithm to evaluate more than 3,000 primer pair designs based on more than 60 different design criteria in less than two minutes to find the optimal primer pair designs to detect and quantify a given miRNA or other small RNA.

"Researchers can basically paste in their own sequences that they found, and this software will rapidly design assays for these new sequences," Pfundheller said.

Exiqon's second new software product will allow customers to design LNA probes to detect mRNAs by in situ hybridization. Using this approach, customers can avoid working with "time-consuming and costly generation of riboprobes," Exiqon said in a statement.

Based on mRNA target sequence, the software will evaluate more than 5,000 designs based on more than 20 design criteria in less than a minute, the company said.

"Typically researchers have used riboprobes, and to some extent DNA probes … but today we are selling manually designed probes for messenger RNAs," Pfundheller said. "With this software it is possible for researchers to paste in their own messenger RNA, add the modifications they want, and then place a simple order online."

Exiqon's LNAs are RNA derivatives that contain a ring structure in their backbone, locking the molecules in a specific configuration with an ideal binding conformation. When incorporated into a DNA oligonucleotide, LNA speeds up the pairing with a complementary nucleotide strand and increases the stability of the resulting duplex.

Exiqon has built its business around developing research tools based on its LNA technology, but in recent months it has also put together a stable of bioinformatics software to supplement its molecular biology offerings.

The first of these software products was its ProbeFinder assay design software for the design of LNA probe-based real-time PCR assays for use with the Universal ProbeLibrary, developed by Exiqon and exclusively available from Roche Applied Science.

In addition, in May Exiqon inked a development and distribution deal with MultiD Analyses to incorporate a version of MultiD's GenEx qPCR analysis software for pre-processing and analysis of data from Exiqon's LNA Universal RT microRNA PCR kits (PCR Insider, 5/25/10).

"[W]e have always put a lot of effort into our bioinformatics work," Pfundheller said. "We use and develop assay design software when we develop all of our products. Basically, since we got the LNA technology we have been working on investigating the properties of LNA, and it's all that knowledge … about LNA and its properties … that we take advantage of in our new assay design software."

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