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April 12, 2003

DNA Software Receives NIH SBIR Phase II Grant to Develop Advanced, High-throughput PCR Design Software

Ann Arbor, Mich. – April 12, 2003 —The National Institute of Health (NIH) has awarded DNA Software a Small Business Innovation Research Program (SBIR) Phase II Grant to enhance its existing Oligonucleotide Modeling Platform™ (OMP™) to develop advanced, high-throughput PCR design software.

The grant will help the company develop new software for designing PCR in various formats based upon a rigorous scientific and computational approach. This new software will significantly improve the reliability of PCR and will enable high-throughput PCR applications resulting in significant cost savings. The developed software will include the ability to optimize reaction conditions in silico and utilize a rigorous equilibrium model for hybridization in order to predict the product distribution after each step of PCR.

DNA Software’s proposal, led by Dr. Svetlana Morosyuk, research director, and Dr. John SantaLucia, founder and chief scientist, was classified as “Outstanding” by its scoring committee. According to Dr. SantaLucia “We achieved excellent results from our Phase I and the preliminary work we’ve done on kinetics points to continued success.”

Many of the software advancements developed through the grant will appear in DNA Software’s commercial software prior to the expected grant completion in early 2004. “From the start we developed OMP so that the core science engine could be continually improved without affecting the various interfaces we develop,” says Donald Hicks, company executive vice president, “so already version 3 of Visual OMP, to be released this June [2003], will benefit from the award.”

The award will fund three specific aims:

  • OMP core development. Tools for optimizing assay conditions for common PCR formats will be developed and a kinetics simulation model will accurately predict the product distribution at the end of thermocycling. In addition, the ability to compute large-scale simulations will be further extended.
  • Develop a generalized GUI and internal functionality for PCR in different formats. The graphical user interface will be extended to support simulation and optimization of PCR in different formats. The first templates developed will focus on multiplex PCR, gene synthesis PCR, real-time PCR, and mismatched-primer PCR.
  • Experimental studies for kinetics parameterization and validation of OMP for multiplex PCR and other formats. DNA Software will collaborate with Dr. Nils Walters at the University of Michigan to perform a systematic study of the kinetics (time course) of PCR using the advanced fluorescence spectroscopy and stopped-flow kinetics equipment available in Dr. Walters lab. The company will also validate the predictions of our software for PCR primer design with a carefully designed series of experiments.

About DNA Software, Inc.
DNA Software, Inc. combines science and software to enable industrial genomics through advances in technologies based on nucleic acids. The company’s first software platform, OMP™ (Oligonucleotide Modeling Platform™), models in silico the folding and hybridization of single-stranded nucleic acids with great accuracy. The company combines OMP™ with scientific consulting, custom software development, and custom laboratory research to deliver state-of-the-art support for designing and developing of nucleic acid based technologies.

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“We find it [Visual OMP™] makes very accurate and sometimes surprising (but true) predictions about binding efficiency in multiplexes...” David Whitcombe, Chief Scientific Officer, DxS Ltd, UK.
“It [Visual OMP™] is very powerful software when used for multiplexing design...” Chris Novak, Ambion
“I have designed over 10,000 PCR assays in my experience with DNA Software’s Visual OMP™ and found greater than 95% success rate when using it to design my assays compared to less than 20% success without it.” Dr. Eric Bruening, MolecularMD
“I have been using DNA [Software™] for a long time, at least 8 years. I want to have the best tools available and that is why we use it.” Dr. Nancy Schoenbrunner, Roche Molecular Systems
“I am a long-term user of Visual OMP™. I like this program very much because it provides a solid scientific basis for oligo design and cuts the development time by more than half.” Olga Budker, longtime Visual OMP user
“In my experience, DNA Software™ saved me 75% of my oligo costs.” Helen Minnis, Wave 80
“DNA [Software™] has passed my tests. I’ve recommended it [Visual OMP™]. It performs extremely well.” Dr. Ned Sekinger, Luminex Corporation
“Learning to use the program [Visual OMP™] is time well spent, and the support staff at DNA Software is always ready and able to help” Dr. Sue J. Kohlhepp, Providence Portland Medical Center.