Consensus Tm Predictor

Nearest-Neighbor Thermodynamics

The nearest-neighbor model treats DNA duplex stability as the sum of stacking interactions between adjacent base pairs. Each of the 10 unique dinucleotide combinations (AA/TT, AT, TA, CA/TG, GT/AC, CT/AG, GA/TC, CG, GC, GG/CC) has experimentally determined enthalpy (ΔH) and entropy (ΔS) values.

Three major parameter sets exist: SantaLucia (1998) unified parameters from seven labs, Sugimoto (1996) from direct calorimetric measurements, and Breslauer (1986) from early UV melting studies. Each set was derived from different experimental conditions and analysis methods, leading to systematic differences in predictions.

The SantaLucia table also includes initiation parameters that depend on the terminal base pairs (AT vs GC termini), while the Sugimoto and Breslauer tables use zero initiation. Self-complementary (palindromic) sequences receive an additional symmetry correction of −1.4 cal/mol·K to the entropy.

Salt Correction for Tm Prediction

Cations neutralize the negatively charged phosphate backbone, stabilizing the DNA duplex. Higher salt concentration raises Tm significantly — moving from 10 mM to 1 M Na+ can shift Tm by 20–30°C.

This tool uses the simplified Owczarzy correction: ΔTm = 16.6 $\times$ log10([Na+]). This approximation works well for monovalent cations in the 10–1000 mM range. For buffers containing Mg²⁺ (common in PCR), Tm may be 2–5°C higher than predicted.