Why aren't the amine groups in the nucleic acid bases protonated? Nucleobases G, C and A carry an amine group ($\ce{-NH2}$). In amino acids, the amine groups are considered protonated at physiological pH. Why isn't it the case for the amine groups of nucleobases?

I found some references discussing the protonation of nucleobases, but I am not enough expert in either DFT (http://www.ncbi.nlm.nih.gov/pubmed/19049279) or Mass Spectrometry (http://www.ncbi.nlm.nih.gov/pubmed/17920289/) to  get a rational from this. Plus, neither they nor the references they cite and that I have briefly examined actually consider protonation of the amine groups.
There are 2 answers:


As f' answered, the amino (NH2) group in a nucleobase is conjugated
with the heterocycle. Therefore, its pKa is closer to the one of
aniline. In other words, it is much less basic than an alkylamine.
Any drawing of a molecule in chemistry or biology is only a mere representation (agreed on by scientists) of the reality. For example, amino-acids are most usually drawn as H2N-R-COOH. We all know that it does not reflect reality but we all use that representation because it is much more readable than +H3N-R-COO- (which itself is also wrong), and because the real form of the amino acid will greatly depend on the experiment conditions. So you must always consider in what medium the molecule is to determine, more or less, its major form.