Oligonucleotides used in gene therapy and silencing are fragile compounds that degrade easily in biological environments. Porous biocompatible carrier particles may provide a useful strategy to deliver these therapeutics to their target sites. Development of appropriate delivery vehicles, however, requires a better understanding of the oligonucleotide-host interactions and the oligonucleotide dynamics inside carrier particles. We investigated template-free SBA-15 type mesoporous silica particles and report their loading characteristics with siRNA depending on the surface functionalization of their porous network. We show that the siRNA uptake capability of the particles can be controlled by the composition of the functional groups. Fluorescence recovery after photobleaching measurements revealed size-dependent mobility of siRNA and double-stranded DNA oligonucleotides within the functionalized silica particles and provided evidence for the stability of the oligonucleotides inside the pores. Hence, our study demonstrates the potential of mesoporous silica particles as a means for alternative gene delivery in nanomedicine.