Chemical reactions involved in staining
Alizarin red S can stain calcium deposits through interaction of its sulfonic acid and hydroxy groups with calcium ions.

I found a reference for you: http://jhc.sagepub.com/content/17/2/110.full.pdf+html

Interestingly, however, this research seems to suggest using a solution of pH $\approx$ 9, stating that solutions of acetic acid (pH 5) did not work that well.