The present invention concerns a system for isolating, depleting, or separating a targeted nucleic acid, such as rRNA, from a sample comprising targeted and nontargeted nucleic acids. It effects a way of enriching for nontargeted nucleic acids, such as mRNAs. The invention further concerns methods of implementing the system and kits for implementing the system, which involves at least one bridging nucleic acid comprising 1) a targeting region complementary to a region on the targeted nucleic acid and 2) a bridging region complementary to the capture region of a capture nucleic acid that comprises a nonreactant structure. The nonreactant structure can be used to isolate the hybridizing molecules after incubation under conditions that allows hybridization.
