Melting temperature is the temperature at which 50% of the oligo and its
perfect complement are in duplex.
PCR annealing temperature
a few degree (46) lower than the melting temperature is usually used to increase
the probability of primer binding.
To calculate melting temperature or for more information, please
see BioToolKit or Primo Online.
Simple rule
Melting temperature (T_{m}) = 4 * Number of G or C + 2 * Number of A or T (°C)
Nearest Neighbor
The Nearest N predicts melting temperature using the "Nearest Neighbor" model (Jhon SantaLucia, Proc. Natl. Acad. Sci. Vol. 95, p14601465 (1998)),
which is more accurate.
Alternative model
Calculations using the following formula
T_{m} = 64.9 + 41 * (Number of G & C  16.4)/oilgo length 
500/oligo length (°C)
are usually in agreement (± 3 °C) with the results using the Nearest Neighbor model.
Correction for salt
T_{m}([Na^{+}])
= T_{m}(1M NaCl) + 11.7 * log_{10}([Na^{+}]) (°C)
(Jhon SantaLucia, Proc. Natl. Acad. Sci. Vol. 95, p14601465 (1998))
