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Tm Predictor For Longer Sequences

It is a melting temperature predicter for 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 sequence, the salt concentration (taken as [Na+]) and nucleotide strand concentration (taken in g/ml) 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 (which is 70 basepair in this case), the Na+ ion concentration and the nucleotide strand concentration in the given equation.
Tm (°C) = (7.35 × E) + [ 17.34 × ln(Len) ] + [4.96 × ln(Conc)] + [0.89 × ln(DNA)] - 25.42

This gives the melting temperature for a 70 bp window.

↓

The above procedure is repeated for the complete sequence with a step-size of one bp.

Figure:Flow chart to calculate the melting temperature


Table 1. DNA strength parameter value for each dinucleotide step

      Stack →        H-bond
↓
5
3
3
2
RY
YY
RR
YR
4+4
GC =13
CC =11
GG =11
CG =10
1+4
AC = 10
TC = 8
AG = 8
TG = 7
4+1
GT = 10
CT = 8
GA = 8
CA = 7
1+1
AT = 7
TT = 5
AA = 5
TA = 4