It is a melting temperature predicter for short DNA sequences based on a simple phenomenological model of DNA denaturation. It takes into account the stacking and hydrogen bonding interaction (as DNA strength parameter). Length of the sequences, the salt concentration (taken as [Na+]) and nucleotide strand concentration (taken in M) to predict the melting temperature.
Read the DNA sequence from one end to the other
& add up the DNA strength parameter (Given in table 1).
Calculate the strength parameter per base (E) as: E = DNA strength parameter ⁄ Length of sequence
Substitute the value of E, the length of sequence
, the Na+ ion concentration and the nucleotide strand concentration of the solution in the
given equation Tm (°C) = (7.35 ×E) + [ 17.34 ×ln(Len) ] + [4.96 ×ln(Conc)] + [0.89× ln(DNA)]
Figure:Flow chart to calculate the melting temperature