News

February 4, 2010

New Software for Modified Oligonucleotides, Target Accessibility, and Off-Target Amplicons

ANN ARBOR, MI – Feb. 4, 2010 – DNA Software, Inc. is pleased to announce the release of significant updates to its OMP™ (Oligonucleotide Modeling Platform™), ThermoBLAST™, and Modifieds™ software products. These updates now allow users to (1) conduct in silico experiments with oligos containing modified nucleotides, (2) graph of target accessibility and complexity, and (3) detect off-target amplicons and view them in a virtual gel.

DNA Software is a pioneering sciences and software company that is focused on original wet lab research, cutting-edge software development, continuous product improvement, and first-rate customer service. In addition to expert technical support, DNA Software’s customers automatically receive software updates as part of their annual product license.

In Silico Experiments with Modifieds Oligonucleotides:
Oligos with modified nucleotides are commonly used for: designing probes with high sensitivity and specificity, designing siRNAs with high efficacy, and performing assays of epigenetic gene regulation.

DNA Software, Inc.’s unique Modifieds™ module enables you to accurately:

  • predict secondary structure of oligos and targets with modified nucleotides
  • design and optimize hybridization-based experiments that include modified nucleotides
  • scan modified oligos against large genome databases to detect false positives and off-target effects

Evaluating Target Accessibility and Complexity:
Primers and probes designed against targets with a high degree of secondary structure (i.e. low target accessibility) can result in false negatives due to low sensitivity. Conversely, primers and probes designed against targets with low complexity can result in false positives due to low specificity.
DNA Software’s target accessibility and complexity graph within Visual OMP™ indicates relative accessibility and complexity of regions within a target sequence to aid users in designing sequences against optimal target regions.

Detecting Off-Target Amplicons:
PCR primers often hybridize to sequences other than their intended targets. Extensible off-target primer hybridizations may result in the amplification of unintended products during PCR.
DNA Software’s amplicon detector within ThermoBLAST™ uses the genome scanning capability of ThermoBLAST™ to find extensible hybridizations that result in the amplification of off-target amplicons. The amplicon detector then displays all amplicons on a virtual gel, which allows users to quickly verify the specificity of PCR primers without running a gel in a wet lab.

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 its 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 prediction of nucleic acid secondary structure plus the design, simulation, and optimization of probes/primers, RT-PCR, qPCR, Multiplex PCR, Taqman, Beacons, Scorpions, Microarrays, SNP detection, FRET assays, RNAi, LATE-PCR, plus new formats. ThermoBLAST™ quickly and accurately scans DNA, RNA, or modified oligonucleotides against large genome databases, identifies all hybridizations under actual reaction conditions, and detects all extensible, off-target amplicons. The Modifieds™ module adds modified nucleotides (e.g. LNA, PNA, Morpholino, Deoxyuridine-DNA, 5-Methylcytosine-DNA, 2’-O-Methyl-RNA, Phosphorothioate, Inosine, Isocytosine, Isoguanine, plus many more) to OMP™ and ThermoBLAST™. OMP Developer Edition™ (OMP DE™) and ThermoBLAST Developer Edition™ (TB DE™) bring customizable, command line, high-throughput computing power to large assay design and genome scanning projects or enterprise applications.
The company has 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.