Cationic polymers are not the best option for small ODNs. The complex formed for short nucleic acids may not be stable enough. Try lipid-based transfection reagent, or add some carrier plasmid DNA to OND or siRNA to improve the stability of the resulted complex.
A number of issues may cause your problem. Collagen in bovine tendon achille is highly cross-linked and very insoluble in water due to post-translation modifications. Your extract condition might not work as efficiently as you think. Have you measured the protein concentration of the extract? Collagen subunit has high MW, 12% maybe too high. Try 8% or 10% gel instead. 5% only good for HMW assembeled protein complexes.
You asked about the residual organic solvent in samples, did you notice any loss soon after you load your samples into the wells? If so, use dialysis or speedvac to remove it.
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