Calculating Tm value by Nearest Neighbor Method

Calculating Tm value by Nearest Neighbor Method

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Tm value is the temperature at which DNA complementary base pairs deviate by 50%. The Wallece method, GC% method, and nearest neighbor method are well known for calculating this.  The nearest neighbor method is generally acknowledged to calculate a value closer to the actual measurement.

When you are using a PCR enzyme that is compatible with 2 step PCR cycle including our PCR enzymes in the product BCF4050, please use the nearest base pair method to calculate Tm value.

The 1st primer design tool (Excel VBA file) in our download section uses the thermodynamic parameters (ΔH °, ΔS °) listed in Table 2, Nearest-neighbor thermodynamics in Reference 1 below are used to calculate Tm value .


  1. Breslauer, K.J. et al. (1986) Proc. Natl. Acad. Sci. USA. 83: 3746-3750.
  2. 最近接塩基対パラメータを用いた核酸の安定性予測とその機能との関係
    杉本 直己 生物物理 vol33.p61-67 吉岡書店