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July 22, 2009

DNA Software, Inc. Awarded NIH Funding to Develop Pioneering Nucleic Acid-Based Technologies

ANN ARBOR, MI – July 22, 2009 - DNA Software, Inc. has been awarded three Fast Track SBIR grants from the National Institutes of Health to develop original in silico technologies to predict 3D structures of RNA-based molecules, improve diagnostics via modified nucleotides, and model the reaction rates of DNA and RNA experiments. The company successfully completed its milestones for Phase I of each project and recently began work on Phase II.

DNA Software, Inc. is a unique life sciences technology company that conducts original wet lab research, develops advanced bioinformatics tools, sells molecular biology software, offers structural biology services, and provides advanced scientific consulting. DNA Software’s products and services improve the work of scientists who conduct nucleic acid-based research.

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Nucleic acids, commonly known as DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid), are the molecular building blocks of life, form the basis of genetic blueprints, and direct activities in living organisms. DNA Software’s tools help scientists to quickly and accurately develop new medical solutions from this nucleic acid information.

In Silico 3D Structure Prediction to Improve and Accelerate Drug Discovery
The genomics era has produced a flood of interesting macromolecular sequences, but there is a shortage of corresponding 3-dimensional (3D) structural information. As a result, there is a lack of structural understanding of the mechanism of the vast majority of known nucleic acid sequences. Half of all clinically used antibiotics target bacterial ribosomes, which are RNA-based molecules. Yet, the 3D structures for the complete ribosomes of many pathogenic bacteria are still unknown. Thus, the ribosome represents an important target for structural prediction and future drug development, including antibiotics for pathogenic bacteria that have developed drug resistance.

DNA Software has a breakthrough technology, called Nucleic Acid CAD™ (NA-CAD™), which expands nucleic acid sequence information into all-atom 3D structure predictions of diverse RNA-based structures with near-crystal structure accuracy. With this NIH project, DNA Software is modeling ribosome structure and function and aims to predict the 3D structures of complete ribosomes of clinically relevant pathogens.

Novel Software for Modeling PCR Reaction Rates and Diagnostics with Modified Nucleotides
While current software programs can model the thermodynamics (i.e. the results at equilibrium after a long time) of DNA and RNA reactions, none can model the kinetics (i.e. how fast the reaction takes place). In addition, most software can only model DNA or RNA. None can accurately model the large variety of modified nucleotides that are added to or replace DNA and RNA sequences to increase the sensitivity and specificity of nucleic acid-based diagnostic tests and therapeutics. DNA Software is combining the unique features of kinetics and modified nucleotides with its existing OMP™ (Oligonucleotide Modeling Platform™) software to create a first-rate tool to develop ultra-fast, sensitive, and selective diagnostics. OMP™ has become the gold standard for assay development. It is utilized by prominent research organizations from around the world and across many industries (e.g. biotech, pharmaceutical, diagnostics, biodefense, reagents, government, academic, and institutes).

DNA Software recently released its first software product for modified nucleotides. The Modifieds™ software module allows users to simulate and design assays that incorporate modified nucleotides within the OMP™ program. Modifieds™ currently includes LNA, PNA, DeoxyU, Morpholino, Inosine, Iso-C, and Iso-G. DNA Software is currently deriving additional thermodynamic parameters for many more modified nucleotides in its wet lab. These parameters will be released to each customer as they become available and as part of the Modifieds™ software license. Modifieds™ is a unique product on the market. Leading research organizations, including the Centers for Disease Control and Prevention, are utilizing Modifieds™ to improve their assay development.

About DNA Software, Inc.
DNA Software, Inc. was founded in 2000 to commercialize the advances in nucleic acid chemistry discovered by world-renowned expert Dr. John SantaLucia, Jr. (the company’s Chief Scientific Officer). DNA Software’s technologies have become the standard of excellence for nucleic acid research and diagnostics development.

DNA Software is a unique software company considering that it conducts original wet lab research. The company’s software programs are the most accurate and comprehensive tools available because their advanced algorithms and models are driven by a large database of thousands of diverse, wet lab-derived, experimental results. DNA Software’s tools correctly design and simulate complicated experiments on the first attempt. Customers can simulate thousands of experiments with the software before running a single experiment in a wet lab. Thus, DNA Software’s technologies save customers significant time, resources, and money that would have been wasted on trial-and-error experimentation.

DNA Software offers contract research, custom software development, commercial web applications, and scientific consulting for nucleic acid research. The company also licenses packaged software tools that help scientists quickly and accurately develop new assays, diagnostics, and therapeutics. OMP™ (Oligonucleotide Modeling Platform™), the core engine that runs all of DNA Software’s tools, models in silico the folding and hybridization of nucleic acids with exception accuracy. Visual OMP™ is a platform program for the design, simulation, and analysis of probes/primers, RT-PCR, qPCR, Multiplex PCR, Taqman, Beacons, Scorpions, Microarrays, SNP detection, FRET assays, RNAi, LATE-PCR, plus new formats. OMP Developer EditionTM (OMP DE™) brings customizable, command line, high-throughput computing power to large assay design projects or enterprise applications. ThermoBLAST™ quickly and accurately scans DNA and RNA against genome databases, identifies all off-target hybridizations, and tells you if these mishybridized probes/primers are extensible by polymerase. Modifieds™ allows you to simulate and develop assays that incorporate modified nucleotides (e.g. LNA, PNA, Morpholino, DeoxyU, Inosine, Iso-C, and Iso-G).

The company has recently expanded its original DNA and RNA-based, molecular biology solutions to include modified nucleotides, oligonucleotide kinetics, and structural biology.

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Thursday, 06 November 2014 22:15

DNA Software introduced the full commercial release of ThermoBLAST Cloud Edition (TB-CE). TB-CE provides a new standard for evaluating the target specificity of oligonucleotides.  Click here to learn more.  

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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.