May 6, 2008

DNA Software Solves 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”.


  1. 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.
  2. 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.
  3. 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.
  4. Spink, C. H., Garbett, N. and Chaires, J.B. (2007) "Enthalpies of DNA melting in the presence of osmolytes", Biophysical Chemistry, 126, 176-185.
  5. 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.
  6. 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.

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