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Figure 1: Comparison of
experimental versus Visual OMP predicted free energies. Note the high
correlation of 0.98 between actual experimental results and Visual OMP
predictions. Fifteen percent of the
experimental data in this plot contained the buffer used in bead hybridization
technologies marketed by Luminex, Inc. TMAC Study Summary: DNA Software is pleased to announce
the addition of a free energy correction term for the oligonucleotide
duplex stabilizing agent Tetramethylammonium Chloride
(TMAC) to its Oligonucleotide Modeling Platform. The equation for this added functionality was
derived from experimental UV melting curves of 52 duplexes, having a range of
lengths and G+C compositions, in buffers containing TMAC concentrations from 15
mM to 3M TMAC, sodium concentrations ranging from 0.066 to 1.03 M, and
magnesium concentrations up to 2 mM. A marked improvement over the
predictive equations from the literature, Visual OMP can now predict DGº37 and Tm to within 0.42 kcal/mol and 2.5º C,
on average, upon addition of TMAC to the buffers of various PCR, Bead, and
Microarray technologies, including those employed by Luminex,
Inc.1-4 This added
functionality to Visual OMP is representative of DNA Software's commitment to
provide our customers with the most current scientific advancements in
oligonucleotide modeling and design for the genomic-based assays of the present
and the future. This work was supported
by NIH SBIR grant # R44 GM076745. References 1. Diaz,
M.R. and Fell, J.W. (2004) High-Throughput Detection of Pathogenic Yeasts of the Genus Trichosporon.
Journal of Clinical
Microbiology, 42(8), 3696-3706. 2. Chevet, E., Lamaitre, G. and Katinka, M.D. (1995) Low concentrations of tetramethylammonium chloride increase yields and
specificity of PCR. Nucleic Acids
Research, 23, 3343-3344. 3. Kovarova, M. and Draber, P.
(2000) New specificity and yield enhancer of polymerase
chain reactions. Nucleic
Acids Research, 28(13), e70. 4. Wong,
C.W., et al. (2007) Optimization and
clinical validation of a pathogen microarray. Genome Biology,
8(5), R93.
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. For more information on DNA Software, Inc.,
visit our website at http://www.dnasoftware.com or contact us. CONTACT: DNA Software, Inc. | ||||||||||||||||||||||||||||||||||||||||||||||||||||
