How is the Tm calculated in LGC Biosearch’s Technologies' RealTimeDesign™ software?
Our RealTimeDesign™ (RTD™) uses the SantaLucia "unified" nearest neighbor thermodynamic parameters in the algorithm to calculate melting temperature (or TM). There are often discrepancies between the TM values predicted using RTD and those of other programs due to different thermodynamic values and also different concentrations for the assay components. These differences are further explained in the following reference: Comparison of different melting temperature calculation methods for short DNA sequences. Alejandro Panjkovich and Francisco Melo. Bioinformatics 2005 21(6):711-722; 2004 doi: 10.1093/bioinformatics/bti066
For more information, consider the publication: "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics", by John SantaLucia, Jr.
We also recommend a general web tool to model oligo binding called DINAMelt, which can be adapted to a variety of experimental conditions. DINAMelt draws upon the same SantaLucia thermodynamic values as RTD, and a description of its algorithms may be found in the following publication: DINAMelt web server for nucleic acid melting prediction. Markham NR, Zuker M. Nucleic Acids Res. 2005 Jul 1;33:W577-81.