September 7, 2006

DNA Software Awarded NIH Grant to Study Modified Nucleic Acids

Ann Arbor, Michigan - September 7, 2006 – DNA Software has been selected for a Grant issued by the National Institute of Health (NIH). The fast track grant, entitled “Database for Modified Nucleotides, Fluorophores and Additives” has been approved for Phase I and Phase II funding. Phase I, scheduled from November 1, 2005 to May 1, 2006, has recently been completed. Phase II is scheduled to start October 1, 2006.

Phase I
In Phase I of this project survey measurements on morpholino modified oligonucleotides and on 5-methylisocytosine and isoguanine match and mismatch duplexes have been performed. These measurements form the basis for the design of some of the experiments for phase II.

Previously determined effects of glycerol on nucleic acid denaturation have been incorporated into Visual OMP™. The last phase I accomplishment was to add previously determined parameters for deoxyinosine substitutions in DNA duplexes to Visual OMP™; these will be available to Visual OMP™ users in the next update.

Phase II
Besides completing the morpholino:RNA match, Morpholino:RNA dangling end, and iC and iG thermodynamic parameter databases in phase II, systematic measurements will be made to also complete the thermodynamic parameter database for PNA. These measurements include PNA:RNA matches, PNA:PNA matches, PNA hairpins, PNA:DNA mismatches and PNA:DNA dangling ends.

The other Phase II goals include completing the thermodynamic parameter database for 18 commonly used labels (fluorophores, quenchers, and biotin), and determining the thermodynamic corrections for duplex stability as a function of concentration for the additives DMSO, Betaine, SYBR-Green, TMAC, and formamide.

Lastly, these newly determined parameters and dependencies will be incorporated into Visual OMP™, and a module to design custom probes with modified nucleotides will be developed.

DNA Software expects Phase II to be completed by October of 2007. Astrid Tuin, DNA Software's lab director states that “The Phase II experiments, analysis of the data and software development are carefully planned, so we expect phase II of this exciting project to go smoothly. All of the goals should be accomplished on time.”

Background and significance of the project
Well designed morpholino oligonucleotides can be used as an efficient and specific oligonucleotide-based antisense reagent in the field of functional genomics to match biological function(s) with gene sequence.

The pairing capability of iC and iG has been employed for molecular recognition and site-specific incorporation by DNA polymerase. In complex assays where high levels of natural DNA of known or unknown sequences exist, the orthogonal pairing capability of iC-iG allows for specific molecular recognition to take place without interference.

PNA has excellent properties, like chemical and biological stability, enhanced hybridization affinity to DNA and RNA, and incorporation of non-natural nucleobases, that can be used for diagnostics, antigene and antisense therapies, and antiviral and antimicrobial PNA therapies.

By determining the thermodynamic influences of labels (fluorophores, quenchers) and different additives, Visual OMP™ can help improve design of (multiplex) Real Time PCR assays, leading to higher efficacy and specificity.

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.

Not finding what you’re looking for? Let us help. Click or Call +1.734.222.9080

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.  

read moreView All News & Events
“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.