RNA protein complex interaction in 4-12% NU PAGE gradient gel - RNA PROTEIN bEHAVIOR IN GRADIENT GELS (Aug/11/2011 )

Hi there
I am facing problem related to the resolution of RNA protein complex on NU PAGE gradient gel(4-12%).The organic phase ( RNA-protein complex) shows high resolution whereas the aqueous phase(MS2 MBP tagged RNA ) shows poor resolution on the 4-12% NU PAGE gradient gel after staining with commassie blue.Can anybody guide me how can I get equally good results for both phases.

Wild guess - There are two types of buffers with the NuPAGE 4-12 - MES and MOPS buffer. MES gives you better resolution in the lower molecular weight area and MOPS higher.
One other thing that I experienced with my gels is when you run it at 200v as suggested and if your buffer or gel is old (or buffer reused many times) gel gets overheated and the structural integrity of the gel screws up (i have even seen the old 2-year old gel boiling) that may also be something. I usually run my gels at cold room and run it around 150 and get good resolution for my protein with the MOPS buffer.