Prior to mixing with lipofectamine during transfection, if I sonicate the GFP plasmid for 30-60 seconds, will it still be able to get expressed in the cells?
My experiment involves nanoparticle coated DNA. I do not sonicate naked DNA but to prevent aggregation, I sonicate the nanoparticle coated DNA briefly for 30-60 seconds prior to lipofectamine treatment. As I am detecting fluorescence using these sonicated NP/DNA, one of the possible explanations could be that some unreacted free DNA is complexing with lipofectamine and getting expressed. However, if 30-60 seconds sonication is enough to disrupt expression of naked plasmid, then it could rule out the above explanation.