Problems We Solve

DNA Software® long been recognized as the “gold standard” for primer and probe design; providing solutions for difficult and high level multiplexes. In addition to design, DNA Software has made a breakthrough in the fundamental understanding of PCR and has incorporated this breakthrough, “Counting PCR” , into its PCR analysis tool qPCR CopyCount.
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Absolute Quantification

The problem with obtaining Absolute PCR Quantification currently is the need to laboriously prepare standards or run a standard curve. Analysis of qPCR has traditionally calculated a Ct (or Cq) value, which are hard to interpret. Our new product, qPCR CopyCount™, allows for any qPCR curve to be analyzed determining the absolute number of copies of DNA at cycle zero and directly provides the DNA copy number.

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PCR Design

The problem with PCR based design is that it is difficult to achieve high assay sensitivity and specificity due to obstacles such as primer dimers, false hybridization and competing secondary structure. These issues only magnify as the multiplex size increases. Better design makes a difference. VisualOMP improves assay sensitivity by accurately predicting the secondary structure and locating the sites on the target that are most thermodynamically accessible. Assay specificity is compromised by false positive hybridizations, which are minimized by ThermoBLAST. Multiplexing applications are particularly sensitive to design where the best practice is to design primers that amplify their targets with equal efficiency and with minimal cross-reactivity.

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False Positives

The most common cause of false positives in PCR is the formation of false amplicons due to primer mishybridization. Similarly, for Antisense and siRNA oligonucleotide therapeutics, a major cause of side effects is off-target hybridization. ThermoBLAST solves the problem of primer and probe hybridization by scanning against whole genome databases such as the human micorbiome, soil bacterial, respiratory flora and gut flora. BLAST scores hits incorrectly using sequence similarity rather than using the proper rules for match and mismatch complementarity. In contrast, ThermoBLAST uses the proper thermodynamic model which detects 100% of the false positive hits, whereas BLAST detects <15% of thermodynamically stable hits.

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Our Latest

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.