what are factors affect the DNA-Protein interaction,beacuse i am working for the DNA-protein(green fluorescence) interaction complex analysis but formation of complex very less (used interaction analysis by EMSA).
Please elaborate - are you interested in testing if GFP alone interacts with the DNA of your interest?
If you have, on the other hand, expressed fusion products with proteins of your interest and GFP is simply used as a tool, that would be a different matter.
In general, with due precautions, EMSA results provide fairly good information.
If you can use an oligonucleotide as the binding partner, then fluorescence polarization is a very nice technique for measuring the affinity of a fluorescently labeled oligo to a protein. When the oligo binds to the protein, the fluorescence polarization usually increases. This can be measured with a suitably-equipped spectrofluorometer or fluorescence plate reader.
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