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MD Parameter based Tm Predictor

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).

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Calculate the strength parameter per base (E) as:
E = DNA strength parameter ⁄ Length of sequence

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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) = {(-8.69 × E) + [ 6.07 × ln(Len) ] + [4.97 × ln(Conc)] + [1.11 × ln(DNA)]} - 233.45

This gives the melting temperature for a 70 bp window.

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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.Energy Parameters for dinucleotides derived from molecular dynamics simulations(kcal/mol).

Dinucleotide Hydrogen Bond Stacking Energy Strength Parameter
AA -6.92 -26.92 -33.84
AC -9.64 -27.89 -37.51
AG -8.78 -26.91 -35.69
AT -7.05 -27.33 -34.38
CA -9.34 -27.23 -36.57
CC -44.84 -26.33 -38.17
CG -11.37 -27.83 -39.20
CT -8.78 -26.91 -35.69
GA -10.12 -26.98 -37.10
GC -12.03 -28.27 -40.30
GG -11.84 -26.33 -38.17
GT -9.64 -27.87 -37.51
TA -7.16 -27.15 -34.31
TC -10.12 26.98 -37.10
TG -9.34 -27.23 -36.57
TT -6.92 -26.92 -33.84