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”.
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