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April 1, 2011

DNA Software, Inc., awarded an NIH SBIR fast track grant for the development of “An Antisense Design and Simulation Platform”

In this grant proposal "An Automated Antisense Design and Simulation Platform", a comprehensive molecular diagnostics software tool that is specific to the design and simulation of antisense oligonucleotide analog probes will be developed. The application of antisense technologies to the study of human diseases has been proven in the literature for cancer, immune deficiency disorders, diabetes, muscular dystrophy and cardiovascular disease, hepatitis A and C, HIV, SARS-coronovirus, Ebola, Dengue Fever, paramyxoviruses (measles), and the West Nile virus. However, the progress of directed antisense research has been slow due to the absence of antisense oligonucleotide analog thermodynamic and kinetic databases, and because the currently used rule-of-thumb design strategies rarely ever initially produce effective probes. Many researchers are then forced to design a small library of probes against the same genomic target to increase their likelihood of success, which is very costly in both time and financing. The proposed Antisense Design and Simulation Platform will enable the researchers of human diseases by providing a tool for the directed research and evaluation of human and viral genomic targets so that rationally designed antisense oligonucleotide analogs may be used as a molecular diagnostics tool.

The developmental strategies for producing the proposed platform are to update existing thermodynamic and kinetic databases and to deploy them on the Antisense Design and Simulation Platform, as outlined in the following specific aims: Aim 1.1: Perform 16 thermodynamic melts each for the fluorophore, biotin and quencher labeled PNA and morpholino antisense probes, and for the phosphorothioate/LNA antisense gap-mer probes to demonstrate the feasibility of applying the nearest-neighbor thermodynamic model to these systems. Aim 1.2: Add the thermodynamic parameters determined in Aim 1.1 to the existing PCR platform Visual OMP to demonstrate the feasibility of applying design and simulation algorithms to modified antisense oligonucleotide analogs. Aim 2.1: Complete the thermodynamic library for the fluorophore, and quencher labeled PNA and morpholino antisense probes, and for the phosphorothioate/LNA antisense gap-mer probes. Aim 2.2: Perform kinetics experiments on modified morpholino/RNA and PNA/RNA duplexes, and develop predictive mathematical models for the rates of Morpholino/RNA and PNA/RNA hybridization and unfolding. Aim 2.3: Engineer a fully automated Antisense Design and Simulation Platform that will allow researchers to design specific and sensitive antisense probes with minimal user inputs. By the end of this project a fully automated Antisense Design and Simulation Platform will have been designed, tested, and debugged, and made available to antisense researchers for the purpose of beta-testing the commercial product.

PUBLIC HEALTH RELEVANCE: This project will directly impact public health by providing a comprehensive software tool for the design and simulation of antisense oligonucleotide analog probes, where no other comprehensive antisense software tools exist. The efficacy of applying antisense technologies to human diseases has been proven, using a trial-and-error approach to a number of human diseases, such as: cancer, immune deficiency disorders, diabetes, muscular dystrophy and cardiovascular disease, hepatitis A and C, HIV, SARS-coronovirus, Ebola, Dengue Fever, paramyxoviruses (measles), and the West Nile virus. The proposed Antisense Design and Simulation Platform will benefit the researchers of human diseases by providing an optimized molecular diagnostic tool for the directed research and rational evaluation of human and viral genomic targets.

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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.