The interactions between DNA purines (guanine and adenine) and three ruthenium ammine complexes (hexaammineruthenium (III) chloride, hexaammineruthenium (II) chloride, and ruthenium-red) were studied in a confined environment, within sol-get silica matrixes. Two encapsulation methods were rehearsed (differing in temperature and condensation pH), in order to analyze the effects of the sol-gel processes on the purines and on the Ru complexes separately. The extent of decomposition of the Ru complexes, as well as the interactions established with the purine bases, proved to be determined by the coencapsulation method. Combined results by diffuse reflectance UV-vis and infrared spectroscopies showed that, when coencapsulation is carried out at 60 degrees C, specific H bonding interactions are established between the ammine group of Ade and the ammine groups of the Ru complex or the hydroxo group of an early decomposition product. These are responsible for the important role of the purine in inhibiting the oxidation reactions of the Ru(II) and Ru(III) complexes. In contrast, Gua establishes preferential H bonds with the matrix (mainly due to the carbonyl group), leading to higher yields in the final oxidation products of the Ru complexes, namely, trimers and dimers. Direct covalent bonding of either purine to the metal was not observed.