Author: wahost
DNA team to Present Oligonucleotide Hybridization
Ann Arbor, Mich. – March 8, 2003 — Dr. Svetlana Morosyuk, DNA Sofware director of research, will present DNA Software’s scientific and software advancements like Oligonucleotide Hybridization as they relate to gene quantification at Cambridge Healthtech’s “Profiling PCR and Beyond” in Baltimore, Maryland.
Dr. Morosyuk will present DNA Software’s latest version of in silico environment, Visual OMP™, that is useful for designing gene quantification assays involving PCR, DNA probes, and microarrays. Visual OMP™ uses a comprehensive model of nucleic acid thermodynamics and includes algorithms for calculating the concentration of all species in an assay at any temperature. Visual OMP™ also includes the ability to predict an outcome of a single-target PCR reaction. This useful feature accounts for suboptimal primer binding, target folding, and 3’ extendibility of non-desired structures, which may occur during PCR. It allows users to explore the effects of different ingredient concentrations and annealing temperatures. The software can also be used to design and simulate PCR reactions in the presence of probe(s) and multiple primer pairs.
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.
Another Michigan Life Sciences Corridor Award
Ann Arbor, MI – September 8, 2002 — DNA Software finalized the terms of its Michigan Life Sciences Corridor (MLSC) award from the Michigan Economic Development Corporation. The $932,000 investment will be used to develop software to design DNA assays.
DNA Software will use the life sciences corridor award to apply the company’s existing software platform, the Oligonucleotide Modeling Platform™ (OMP™), to the field of assay design. The new software builds on OMP™’s precise modeling engine and will be used by scientists to design assay. These types of studies have many applications including drug target identification, cancer diagnosis, determining drug mechanisms and side effects, and personalized medicine. The company expects to release the software commercially next summer.
This is the first outside investment in the company from life sciences corridor award. “We founded the company hoping to solve real medical problems that affect real people,” says Mark A. Kielb, company co-founder and president. “Having grown exclusively through customer revenues has kept us tightly focused on customer needs. With the MLSC award we can reach new customers in an area which will significantly improve, and sometimes save, people’s lives.” DNA Software was founded in December 2000 by Mr. Kielb and John SantaLucia Jr., Ph.D., an associate professor at Wayne State University.
According to Don Hicks, DNA Software COO and principal investigator of the project, “We are very pleased to receive this investment from the state. DNA Software was started to bring together an integrated approach from the leading science out of John SantaLucia‘s lab from Wayne State University with some of the newest developments in software technology. This investment from the state will enable the development of the premier platform in this area for the simulation analysis and design of the nucleic acid based assays. DNA/RNA hybridization is the backbone of most of the commonly used assay designs out there, including PCR, nucleic acid based probes, and microarrays. The improved ability to predict nucleic acid hybridization should reduce the time to market for designers of existing assay platforms as well as improving the capabilities to test out and deploy new platforms that are necessary to exploit the advantages of a growing and changing market in the genomic area, and to support advancements in personalized medicine.”
DNA Software’s winning proposal included collaborations with researchers at the Applied Genomics Technology Center (AGTC) at Wayne State University in Detroit, and the Michigan Center for Biological Information (MCBI) at the University of Michigan in Ann Arbor. The software will fill a critical gap, according to Dr. Mark Hughes, Director of the AGTC and the Center for Molecular Medicine and Genetics at Wayne State, “We have the instrumentation and skill set to perform array work, but we lack the complex software tools needed to design and test in silico, before the bench work, the thousands of oligonucleotides [small pieces of DNA] that will be printed on the microarrays.”
As part of the collaboration with the AGTC, the software will be leveraged by two exciting on-going clinical studies. In the first, DNA Software will work with Dr. Andrew Sloan, at the Karmanos Cancer Institute, to design assays to aid in distinguishing patients who are receptive to certain cancer therapies from those who aren’t. Dr. Sloan is convinced that “if we can develop such an assay, it will quickly be adopted by the neuro-oncology community as the standard of care for the treatment of these devastating neoplasms.”
In the second project, DNA Software will work with Dr. Roy Baynes, Director of Bone Marrow and Stem Cell Transplantation at the Karmanos Cancer Institute, to develop microarrays that help screen for potential transplant matches using high-resolution HLA typing. “If this strategy proves to be accurate, truly high throughput, and rapid, it promises to shorten the time to donor identification and will both improve outcomes and translate into lives saved,” according to Dr. Baynes.
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.
DNAS Receives NIH Grant to Develop Advanced PCR Software
Ann Arbor, Mich. – April 2, 2002 — The National Institute of Health (NIH) has awarded DNA Software a Small Business Innovation Research Program (SBIR) Phase I Grant to enhance its existing Oligonucleotide Modeling Platform™ (OMP™) to enable automated high-throughput design of PCR (polymerase chain reaction) primers for amplification of a single target and a simplified multiplex format. The developed software will include the ability to optimize reaction conditions in silico and utilize a rigorous equilibrium model for hybridization which will be used to predict the product distribution after each step of PCR.
“This is the company’s first federally funded grant,” according to Mark Kielb, company president, “and we are very excited at the opportunity to apply our detailed knowledge of DNA thermodynamics to the next generation of PCR assays.”
According to Svetlana Morosyuk, DNA Software senior scientist and the grant’s principal investigator, “Single target PCR is very robust and works about 95% of the time. However, reliability drops for more difficult PCR reactions, such as the multiplex format, difficult templates, and high-throughput applications.” DNA Software outlined three specific aims for the grant:
- Develop a graphical user interface specific for PCR design including
- Extend the functionality of OMP for single target and multiplex PCR primer design.
- Perform validation experiments for OMP™ predictions.
The company expects to complete work on Phase I by the end of the summer 2002.
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.
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