Hi,

I'm currently working on an experiment in which I show competitive DNA binding between 2 proteins via an electrophoretic shift mobility assay (EMSA, see attached image). I have been able that protein2 is capable of displacing protein2 from the DNA with this assay.

Moving forward, I am interested in the changes that the DNA undergoes during this displacement. In other words, what is the architecture of the protein1-DNA complex/protein2-DNA complex? I have already tried to use atomic force microscopy (AFM) to address these questions but could not optimize the system to reliably produce high quality images. Thus, I am searching for alternative techniques.

I came across 2D-PAGE analysis and was wondering if anyone would recommend this technique for the application I have described above. If not, are there any alternative methods? Thanks so much!

Best,

Ryan

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