The development of new antiviral nucleic acid-based drugs and the search for their efficient delivery into cells are an urgent task. We developed methods of immobilizing DNA fragments to titanium dioxide nanoparticles with the formation of TiO2∼DNA nanocomposites. It is shown that DNA fragments in nanocomposites retain their ability to form complementary complexes and can be delivered into cells without transfection agents and other methods of exposure. The proposed nanocomposites were shown to be efficient agents to affect target nucleic acids inside cells with an example of inhibition of influenza A virus (IAV) reproduction. The nanocomposites bearing the DNA1 fragment targeted to the 3′-noncoding region of segment 5 (-)vRNA showed a low toxicity (TC50 ≥ 1500 µg/ml) and a high antiviral activity against different IAV subtypes (H1N1, H5N1, and H3N2) in infected MDCK cells (the virus replication was inhibited by up to four orders of magnitude). The IC50 value for nanocomposites was estimated to be 1.5 µg/ml (30 nM for DNA), so its selectivity index was calculated as ∼1000. Control samples, i.e., nanoparticles without DNA fragments and vise versa as well as unbound DNA fragments in the presence of nanoparticles were much less active, if at all. A high site-specificity of the action of designed nanocomposites (∼3000-fold difference between the effect of the nanocomposites containing target-directed DNA and DNA with a random sequence) indicates a pronounced antisense effect. The presented types of nanocomposites can be applied in the thriving technology of drug delivery to achieve high therapeutic and biological efficacy.