  We study the parameter sensitivity of hetero-polymeric DNA within the purview
of DNA breathing dynamics. The degree of correlation between the mean bubble
size and the model parameters are estimated for this purpose for three
different DNA sequences. The analysis leads us to a better understanding of the
sequence dependent nature of the breathing dynamics of hetero-polymeric DNA.
Out of the fourteen model parameters for DNA stability in the statistical
Poland-Scheraga approach, the hydrogen bond interaction
$\epsilon_{hb}(\mathtt{AT})$ for an $\mathtt{AT}$ base pair and the ring factor
$\xi$ turn out to be the most sensitive parameters. In addition, the stacking
interaction $\epsilon_{st}(\mathtt{TA}-\mathtt{TA})$ for an
$\mathtt{TA}-\mathtt{TA}$ nearest neighbor pair of base-pairs is found to be
the most sensitive one among all stacking interactions. Moreover, we also
establish that the nature of stacking interaction has a deciding effect on the
DNA breathing dynamics, not the number of times a particular stacking
interaction appears in a sequence. We show that the sensitivity analysis can be
used as an effective measure to guide a stochastic optimization technique to
find the kinetic rate constants related to the dynamics as opposed to the case
where the rate constants are measured using the conventional unbiased way of
optimization.
