In these experiments, double-stranded, linear DNA sequences were adsorbed into the pores of spherically shaped acid-prepared mesoporous silica (APMS). The lengths of the sequences were either 760 base pairs or 2000 base pairs. DNA adsorption into the interior of the mesoporous material was confirmed using confocal microscopy of sequences containing fluorescently labeled DNA molecules. Additional characterization with N(2) physisorption and powder X-ray diffraction supported this finding. The extent of adsorption was measured at various concentrations using UV-visible spectrophotometry to establish adsorption isotherms. APMS alone adsorbed a negligible amount of DNA; however, exchanging divalent cations such as Mg(2+) and Ca(2+) into the pores of APMS prior to DNA uptake was found to cause a significant amount of DNA to be adsorbed. Using Na(+) caused a lower amount of DNA to be adsorbed. DNA adsorption was also dependent on the pore diameter of APMS. Adsorption increased upon expansion of the pore size of the metal ion-exchanged material from 34 to 54 A; however, no additional uptake was measured by further increasing the pore size to 100 A. The amount of DNA adsorbed could also be significantly increased by using (aminopropyl)triethoxysilane to covalently link ammonium ions to the surface. Postsynthetic modification of the silica surface with aminopropyl groups increased the maximum DNA adsorption to 15.7 microg/mg silica, for materials with pore diameters of 100 A, which is 2 to 3 times more adsorbed DNA than for metal ion-exchanged material. This indicated that DNA binds more strongly in the presence of the ammonium group compared to the metal counterions. Finally, calculation and comparison of Freundlich and Langmuir constants for these adsorption processes indicate that intermolecular interactions between the DNA molecules within the pores are significant when the effective pore diameter is small, including materials with larger pores that were modified with organosilane.