its ok at least you speak 2 languages. I will try to help you. RNA EMSA no shift issues could be several things including:
- Salt (too much / too little) in the Buffer
- Inappropriate pH
- RNA inappropriately made (the binding area for the protein is not there)
- Binding-protein low abundance due to bad protein preparation (degradation of protein? not enough protein?)
Also is this a UV-crosslinking EMSA with denaturing ie b-mercaptoethanol and SDS or is this native non-denaturing EMSA?
Have you tried to optimize your shift with different buffers ie HEPES or Tris? What about different pH conditions? Different salt conditions? MgCl2? Yes there is a lot of optimizing for RNA EMSA
Its probably the toughest of the experiments - its an art
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