Interaction of endogenous protein and transfected biotinylated nucleic acids was tested by transfecting HeLa cells with nucleic acids (2 μg/ml) using JetPrime according to the manufacturer’s protocol. Six hours after transfection, cells were harvested and lysed in TENTG-150 [20 mM tris-HCl (pH 7.4), 0.5 mM EDTA, 150 mM NaCl, 10 mM KCl, 0.5% Triton X-100, 1.5 mM MgCl2, and 10% glycerol, supplemented with 10 mM β-mercaptoethanol and 0.5 mM PMSF] on ice for 30 min. Lysates were centrifuged at 13,000 rpm for 30 min at 4°C. Equal amounts of whole-cell lysates were incubated for 3 hours at 4°C on a wheel with 3 μg (30 μl) Dynabeads M280 blocked overnight at 4°C as described above. After three washes in 20 mM tris-HCl (pH 7.4), 0.5 mM EDTA, 0.05% Triton, 0.1% Tween, 150 mM NaCl, 10% glycerol, and 5 mM MgCl2, bound material was eluted in Laemmli buffer.

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