Author: wahost
DNAS Solves Betaine Thermodynamics for Improved Assay Design
Betaine Thermodynamics for Improved Assay Design
Figure 1: A comparison of experimental versus Visual OMP™ predicted free energies. Note the high correlation of 0.98 between actual experimental results and Visual OMP™ predictions.
Betaine Study Summary:
DNA Software, Inc. is pleased to announce the addition of a free energy correction term for the oligonucleotide duplex hybridization buffer additive betaine monohydrate to its Oligonucleotide Modeling Platform™, including its Visual OMP™ software. The equation for this added functionality was derived from experimental UV melting curves of 63 duplexes, having a range of lengths from 13-24 base pairs with G+C compositions ranging from 23 % to 65 %. The buffers used in this determination contained betaine concentrations from 100 mM to 2.7 M and a variety of sodium and magnesium concentrations.
A marked improvement over the predictive equations from the literature, Visual OMP™ can now predict DGº37 and Tm to within 0.34 kcal/mol and 0.8 ºC, on average, upon addition of betaine to the buffers of various PCR and Microarray technologies.1-6 This added functionality to Visual OMP, in conjunction with that of Tetramethyl-ammonium Chloride (TMAC) released last year, is representative of DNA Software’s commitment to provide its customers with the most current scientific advancements in oligonucleotide modeling and design of genome-based assays. This work was supported by DNA Software’s NIH SBIR grant titled “Database for Modified Nucleotides, Fluorophors and Additives”.
References:
- Ralser, M, Ouerfurth, R., Warnatz, H., Lehrach, H., Yasupo, M. and Krobitsch, S. (2006) “An efficient and economic enhancer mix for PCR”, Biochemical and Biophysical Research Communications, 347, 747-751.
- Wrobel, G, Schlingemann, J., Hummerich, L., Kramer, H., Lichter, P. and Hahn, M. (2003) “Optimization of high-density cDNA-microarray protocols by ‘design of experiments'”, Nuc Acids Res., 31, e67.
- Rees, W.A., Yager, T.D., Korte, J., von Hippel, P. H. (1993) “Betaine Can Eliminate the Base Pair Composition Dependence of DNA Melting”, Biochemistry, 32, 137-144.
- Spink, C. H., Garbett, N. and Chaires, J.B. (2007) “Enthalpies of DNA melting in the presence of osmolytes”, Biophysical Chemistry, 126, 176-185.
- Hong, J., Capp, M.W., Anderson, C.F., Saecker, R. M., Felitsky, D.L., Anderson, M.W. and Record, M.T. (2004) “Preferential Interactions of Glycine Betaine and of Urea with DNA: Implications for DNA Hydration and for Effects of These Solutes on DNA Stability”, Biochemistry, 43, 14744-14758.
- Vasiliskov, V.A., Prokopenko, D.V. and Mirzabekov, A.D. (2001) “Parallel multiplex thermodynamics analysis of coaxial base stacking in DNA duplexes by Oligodeoxyribonucleotide microchips”, Nuc. Acids Res., 29, 2303-2313.
DNAS Exhibits Its Expanding Technology Portfolio
Ann Arbor, Mich. – October 17, 2007 – DNA Software, Inc. exhibited its science and software developments and growing products and services portfolio at the annual MichBio Expo in Lansing, MI.
DNA Software received The Michigan Investment and Commercialization Success Award in 2003. DNA Software is among the select-few, award-winning, start-up companies that successfully commercialized its technology, continues to expand its R&D and commercial offerings, and is working toward diversifying and growing Michigan’s struggling economy.
DNA Software continues to explore opportunities to develop the biotech industry within Michigan. The company networks with local business-accelerator organizations such as the Michigan Economic Development Corporation (MEDC), MichBio, SPARK, and BioArbor. DNA Software has collaborated with, licensed technology from, licensed software to, and provided consulting services to Michigan universities. When Pfizer Inc decided to close its Ann Arbor R&D facility in early 2007, DNA Software attracted, hired, and retained local talent. Moreover, DNA Software has consulting relationships with former Pfizer scientists and continues to seek expertise in the areas of computational chemistry, structural biology, and mathematical modeling. Interested scientists are encouraged to contact DNA Software.
About DNA Software, Inc.
DNA Software is the leading provider of innovative software and consulting solutions for nucleic acid research. DNA Software combines award-winning science with cutting-edge software technology and offers the industry’s most comprehensive, automated, and predictive software for designing accurate DNA and RNA hybridization assays and reducing costly false positives and negatives.
DNAS Completes TMAC Study to Improve PCR Design
DNA Software Completes TMAC Study to Improve PCR Design
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:
- Diaz, M.R. and Fell, J.W. (2004) “High-Throughput Detection of Pathogenic Yeasts of the Genus Trichosporon”,Journal of Clinical Microbiology, 42, 3696-3706.
- 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.
- Kovarova, M. and Draber, P. (2000) “New specificity and yield enhancer of polymerase chain reactions”, Nucleic Acids Research, 28, e70.
- Wong, C.W., et al. (2007) “Optimization and clinical validation of a pathogen microarray”, Genome Biology, 8, R93.
DNA Software Awarded NIH Grant to Improve Probe, Primer Specificity
DNA Software Awarded NIH Grant to Improve Probe and Primer Specificity
Ann Arbor, Michigan – September 29, 2006 – DNA Software has been awarded a fast track grant by the National Institute of Health (NIH) to develop a cutting-edge software prototype, called ThermoBLAST™.
ThermoBLAST™ is a revolutionary new tool that combines the accuracy of DNA Software’s proprietary OMP Nearest Neighbor model with the speed and breadth of the BLAST algorithm to produce a fast yet exhaustive method for genome scale searches. ThermoBLAST™ will be integrated into DNA Software’s OMP™ (Oligonucleotide Modeling Platform™) software resulting in automated design of more specific probes and primers that can be designed more quickly and more economically. ThermoBLAST™ will allow scientists to develop better assays, while saving time and money.
ThermoBLAST™ will make a major positive contribution to the work of public and private researchers worldwide. Scientists who are designing DNA tests to identify or discover the function of important, disease related genes will be able to “test their tests” in a computer, without having to go through the lengthy lab testing process for each assay. The most difficult DNA-based tests are also the most important. There are very small differences between the genetic code of deadly pathogens and harmless microorganisms. ThermoBLAST™ will greatly improve the ability of scientists to design DNA probes that yield consistent conclusive results, and avoid costly false negatives and positives.
This fast track grant, entitled “Development of ThermoBLAST: Improving the Specificity of Probes and Primers,” is scheduled from September 29, 2006 to April 30, 2008.
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 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.
DNAS attends American Society of Human Genetics Annual Meeting.
Ann Arbor, Mich. DNA Software is attending the American Society of Human Genetics Annual Meeting on October 25-29, 2005. This year’s ASHG Annual Meeting is taking place in Salt Lake City, Utah. Several of DNA Software’s senior engineers will be available to answer your questions.
This year’s theme of american society of human genetics meeting is “Realizing the Promise of the Human Genome Project“, which as the ASHG’s president states “..it is relevant to clinicians trying to diagnose and characterize birth defects and developmental disorders; to counselors informing and supporting patients and families about these disorders; to basic scientists trying to decipher the pathogenesis of Mendelian disorders; to geneticists trying to dissect contributions to complex traits; and to all of us trying to translate the wealth of genomic information into function.”
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 Launches Visual OMP 3 Simulating DNA, RNA based Assays
Genomic researchers can now design more specific and sensitive nucleic acid experiments and reduce trial and error bench work with DNAS Visual OMP 3.
Ann Arbor, Mich. – July 10, 2003 – DNAS Launches Visual OMP™ 3 for Designing and Simulating DNA and RNA based Assays. DNA Software, a leading provider of software, scientific consulting and lab research for genomic researchers, announced today the launch of Visual OMP™ 3. This product is the latest advancement of the company’s proprietary Oligonucleotide Modeling Platform™ (OMP™) which provides researchers with an in silico laboratory environment for designing PCR and microarray based experiments. With Visual OMP™ 3, genomic researchers are able to design more sensitive and specific assays and reduce trial and error bench work.
“DNAS Visual OMP™ 3 provides researchers with the ability to automatically design multiple sets of primers and probes that are optimized for specific experiments yet reduce cross-hybridization and mis-hybridization between oligos and targets,” stated Don Hicks, COO and vice president of DNA Software.
Unlike existing software products, DNA Software’s proprietary ThermoBlast algorithms evaluate the thermodynamic energy associated with every possible competitive reaction and predicts the concentration each will form in a reaction. Probes and primers can be tailored to emphasize specificity, sensitivity, melting temperature or length. DNAS Visual OMP™ 3 is the outcome of nearly ten years research by Dr. John SantaLucia, chief science officer of DNA Software and associate professor at Wayne State University.
“We’ve been using OMP to solve real-world assay design problems on a consulting basis for over two years. Visual OMP™ 3 brings together all that we’ve learned about using in silico technology to design better assays with less effort,” noted Mark Kielb, president of DNA Software.
Visual OMP™ 3’s integrated folding engine allows scientists the ability to visualize target and oligo structure much faster than other available products and includes the first sequence dependent hairpin model. Visual OMP™ 3’s in silico laboratory is further enhanced by integration of the third-party tools BLAST and ClustalW.
DNA Software also offers a OMP Developer Edition™ (OMP DE™), that allows programmers to integrate OMP™ into high-throughput applications. OMP DE™ provides an application programming interface (API) for scripting OMP™ access and linking it with existing databases and supports client/server, distributed (GRID), and network installation.
DNA Software’s Visual OMP™ 3 is available for the Windows operating environment. OMP DE™ is available for Windows, Linux, UNIX, and Alpha operating systems.
Academic pricing is available for all products. For more information or to schedule a demonstration, please contact DNA Software at +1 (734) 222-9092.
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 Presents Poster on Visual OMP 3 at Smalltalk
Ann Arbor, Mich. – June 22, 2003 – DNA Software has been selected to present a poster at the upcoming Smalltalk 2003 conference entitled:
New Software for Simulating and Designing DNA- and RNA-based Primers, Probes and Targets.
Abstract: DNA Software’s Visual OMP™ (Oligonucleotide Modeling Platform™), provides an integrated suite of tools that help scientists clearly identify assay design problems and improve primer/probe specificity and sensitivity in their PCR and microarray designs. It is the first software to offer automatic multiplex primer and microarray probe design where cross-hybridization and mis-hybridization between oligos and targets are evaluated thermodynamically and minimized by the software. Key features include integrated visualization of DNA and RNA folding, and proprietary algorithms for calculating the concentration of all species in an assay at any temperature. OMP Developer Edition™ includes a defined scripting language that allows OMP™ to be programmed for high-throughput analyses. The combination of automated design, visualization and analysis provide the ultimate in silico workbench for genomic assay design.
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 Michigan Life Sciences Corridor Award
Ann Arbor, Mich. – May 29, 2003 — DNA Software finalized the terms of its second Michigan Life Sciences Corridor (MLSC) award from the Michigan Economic Development Corporation. $364,000 will be used to commercialize software for microarray and advanced PCR assay design.
DNA Software will use the award to apply the company’s existing software platform, the Oligonucleotide Modeling Platform™ (OMP#153;), to the field of advanced PCR assay design. The new software builds on OMP#153;’s precise modeling engine and will be used by scientists to design microarray experiments.
In 2002, DNA Software received a MLSC Award in the amount of $932,000 to develop software that designs DNA Microarrays.
Donald A. Hicks, the COO of DNA Software expresses his thoughts upon receiving the award. “We are very pleased that the state recognized all of the tremendous progress we have made in the research and development phase during our year one. It’s especially gratifying that after an initial investment the state evaluated that our success and progress was more than sufficient to warrant a further investment to help us commercialize these advances.”
The thrust of this investment from life sciences corridor award is going to help DNA Software get the word out and reach a wider audience, now that a world leading platform in Visual OMP#153;, the only software platform that integrates simulation and design for nucleic acids for a varity of formats, has been developed.
“With this grant, we will be able to focus on commercialization and developing the business and it should result in increased economic activity and job growth for DNA Software, one of the small, but world leading, companies located here in Ann Arbor” states COO of DNA Software Donald A. Hicks.
DNAS recieves NIH Grant to Develop Advanced PCR Software
Ann Arbor, Mich. – April 12, 2003 —The National Institute of Health (NIH) grant to develop PCR software has awarded DNA Software a Small Business Innovation Research Program (SBIR) Phase II Grant to enhance its existing Oligonucleotide Modeling Platform™ (OMP™) to develop advanced, high-throughput PCR design software.
The grant will help the company develop new software for designing PCR in various formats based upon a rigorous scientific and computational approach. This new software will significantly improve the reliability of PCR and will enable high-throughput PCR applications resulting in significant cost savings. The developed software will include the ability to optimize reaction conditions in silico and utilize a rigorous equilibrium model for hybridization in order to predict the product distribution after each step of PCR.
DNA Software’s proposal, led by Dr. Svetlana Morosyuk, research director, and Dr. John SantaLucia, founder and chief scientist, was classified as “Outstanding” by its scoring committee. According to Dr. SantaLucia “We achieved excellent results from our Phase I and the preliminary work we’ve done on kinetics points to continued success.”
Many of the software advancements developed through the grant will appear in DNA Software’s commercial software prior to the expected grant completion in early 2004. “From the start we developed OMP so that the core science engine could be continually improved without affecting the various interfaces we develop,” says Donald Hicks, company executive vice president, “so already version 3 of Visual OMP, to be released this June [2003], will benefit from the award.”
The award will fund three specific aims:
- OMP core development. Tools for optimizing assay conditions for common PCR formats will be developed and a kinetics simulation model will accurately predict the product distribution at the end of thermocycling. In addition, the ability to compute large-scale simulations will be further extended.
- Develop a generalized GUI and internal functionality for PCR in different formats. The graphical user interface will be extended to support simulation and optimization of PCR in different formats. The first templates developed will focus on multiplex PCR, gene synthesis PCR, real-time PCR, and mismatched-primer PCR.
- Experimental studies for kinetics parameterization and validation of OMP for multiplex PCR and other formats. DNA Software will collaborate with Dr. Nils Walters at the University of Michigan to perform a systematic study of the kinetics (time course) of PCR using the advanced fluorescence spectroscopy and stopped-flow kinetics equipment available in Dr. Walters lab. The company will also validate the predictions of our software for PCR primer design with a carefully designed series of experiments.
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.