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Nearest neighbor thermodynamic parameters used for primer design
| −ΔH(pi, pi+1) | −ΔG(pi, pi+1) | |
|---|---|---|
| AA or TT | 9.1 | 1.55 |
| AT | 8.6 | 1.25 |
| TA | 6.0 | 0.85 |
| CA or TG | 5.8 | 1.15 |
| GT or AC | 6.5 | 1.40 |
| CT or AG | 7.8 | 1.45 |
| GA or TC | 5.6 | 1.15 |
| CG | 11.9 | 3.05 |
| GC | 11.1 | 2.70 |
| GG or CC | 11.0 | 2.30 |
ΔH(pi, pi+1) and ΔG(pi, pi+1) are the enthalpy and free energy in kcal/mol required to disrupt the hydrogen bonds between the complementary bases of a paired chain, where pi and pi+1 are bases of primer p at the positions i and i + 1.
