13.1.3 Tm calculation

Tm estimates generated by Primer3

This section provides references for formulas used by Primer3 to calculate melting temperatures for the binding region of a primer. Under Formula you can choose between two different tables of thermodynamic parameters and methods for melting temperature calculation:

• Breslauer et al. 1986. This is used by old versions of Primer3 (until version 1.0.1), and uses the formula for melting temperature calculation suggested by Rychlik et al. 1990.
• SantaLucia 1998. This is the recommended value.

Three different Salt Correction Formula options are available:

• Schildkraut and Lifson 1965 . This is used by old versions of Primer3 (until version 1.0.1)
• SantaLucia 1998. This is the recommended value.
• Owczarzy et al. 2004.

Rough Tm

The rough Tm of a selected region of sequence is dynamically calculated and displayed in the Statistics Tab in the Viewer side panel, and is calculated as per formulas 5.1 or 5.2 . The rough Tm is usually within 1-3° of that calculated by Primer3.

If you select a region of sequence less than 100 bp in length, then the Rough Tm will be displayed as a tooltip as shown in Figure 13.2 .