Visual OMP 6.4.1TM Upgrade Released to All Customers
Ann Arbor, Mich. – May 12, 2008 – DNA Software is pleased to announce the release of Visual OMPTM 6.4.1, which can now simulate assays that include PNA Parameters.
Peptide Nucleic Acid (PNA)
Peptide Nucleic Acids have excellent properties that include enhanced hybridization affinity to DNA and RNA in a nearly salt-independent manner; chemical and biological stability; and synthetic flexibility that allows conjugation of PNA with peptides and fluorophores, desirable pharmacokinetics, and incorporation of non-natural nucleobases. These properties are important to the design of various genomic-based diagnostics, antigene and antisense therapies, as well as antiviral and antimicrobial PNA therapies. A complete set of nearest neighbor PNA/DNA parameters has been determined by DNA Software, Inc. and are available in the simulation module of the company’s Oligonucleotide Modeling PlatformTM (OMPTM).
Currently, DNA Software’s wet-lab is in the process of determining single mismatch discrimination parameters for PNA/DNA to allow for allelic genotyping. More importantly, we are determining a full set of PNA/RNA match as well as single mismatch discrimination parameters so that OMPTM may be used to design PNA probes against coding RNAs to prevent or quantify their expression.
These added parameters to the simulation module of OMPTM will be essential for the elimination of PNA probe sequences that can form non-desired hairpin or homo-dimer structures or cross-hybridize to other PNA molecules in multiplex assays.
DNA Software is a first-rate science and software company that is focused on cutting-edge R&D, continuous improvement, and customer service. DNA Software customers automatically receive free tech support and upgrades, including Visual OMPTM 6.4, as part of their software license.
Visual OMPTM 6.4.1 Upgrade Summary
New Features:
1. Addition of Peptide Nucleic Acid (PNA)/DNA parameters. This is based on hundreds of measurements made at DNA Software. The Tm is predicted within 2 °C, on average.
2. Addition of the modified nucleotide Deoxyuracil in DNA duplexes. This accounts for the thermodynamic differences of dT and dU in DNA with a full nearest neighbor model that gives Tm predictions within 2 °C, on average. This allows users to design primers and probes for target amplicons made using dUTP, which is used to minimize contamination artifacts . This is also useful for designing assays for DNA deamination and methylation.
3. Expansion of sequences containing ambiguity codes. This facilitates the simulation of primers against SNPs that are designated in genomic sequences as amibiguity codes.
4. Many improvements to the DNA Display graphic such as inclusion of solution conditions and improvements to the cycling of suboptimal structure displays.
5. Improvements to various issues in Sequence Editor such as copying and pasting of sequences and sequence modifications.
Enhancements:
1. Improved Numerical Analysis Graph displaying heterodimer in Graph Key.
2. Fixed Restoring Factory settings causing error in Visual OMPTM.
3. Fixed betaine sequence null error when viewing sequences tab.
These new features combined with updated and improved default design strategies create a powerful new Visual OMPTM. For a complete list of all of the features of the new version, please visit our Version History page.
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, OMPTM (Oligonucleotide Modeling PlatformTM), models in silico the folding and hybridization of nucleic acids with great accuracy. The company combines OMPTM 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. For more information on DNA Software, Inc., visit our website at http://www.dnasoftware.com or contact us.
CONTACT:
DNA Software, Inc.
204 East Washington Street
Ann Arbor, MI 48104
Office: +1 (734) 222-9080
Fax: +1 (734) 222-9087
Email: info@dna-software.com