As mentioned before, the NN model allows us to compute the thermodynamic properties of DNA duplex formation starting from the enthalpies and entropies of the elementary motifs that constitute all possible Watson-Crick sequences of DNA. This section describes how to calculate these magnitudes.
The sequence of an -base ssDNA () is given from the end to the one, where = is the base located at the end, = is the base located at the one. can take four different values ( ). The standard enthalpy of hybridization of such sequence ( ) with its complementary strand can be calculated according to,
The last bases of the sequence do not have a complete stacking interaction because they only have one neighbor. This is why the NN model has to introduce the initiation term. This term always adds a constant contribution, which is sequence independent. Moreover, a variable contribution has to be added depending on the type of bases located at the ends: an extra contribution of and must be added if the sequence starts with a -A...- or -T...-; or ends with a -...A- or -...T-. If the molecule has both motifs (start and end) the contribution has to be counted twice. Moreover, if the molecule specifically starts with -TA...- or ends with -...TA-, there is another extra contribution of and to the initiation terms. Table 3.1 summarizes all these cases.
In general, and are considered to be temperature independent, meaning that the change in heat capacity can be neglected ( ). This allows to compute the free energy of formation ( ),
JM Huguet 2014-02-12