I have to identify nuclear proteins that bind to specific gene/s in saffron. We are looking for a protocol/assay that binds/immobilizes the DNA permanently by one end keeping the other end free. The efficiency should be such that at the time of washing the proteins attached to the bound DNA stays while all the other proteins are washed off and when eluting the specific proteins, only the proteins are eluted out while the bound DNA stays. If you please know or use such a technique it will be worth a help.
Totally agree with Misha. your protein I guess will be recombinant type. In that case, design the protein with avidin or streptavidin bound to it. these tags are over 60kDa. and then design the DNA with Biotin tags attached to it. Avidin-biotin interaction is the strongest. So, now while washing your protein of interest won't be washed off.
The above answer is massively flawed.. if you express your proteins with streptavidin tags then try to fish with biotin labelled DNA then you are just pulling out via the strep-biotin binding which we know is near covalent you will not see if your protein of interest has any true affinity for the target sesequence you are using.
Are you looking at native or recombinant protein? Biotinylated DNA is the way forward I would suggest making several DNA constructs of varying length and 2 versions of each with biotin at each end (but not both) bind the biotinylated DNA to avidin beads then incubate the lysate (nuclear extract for native, bacterial for recombinant)..wash the beads with an elution buffer containing increasing salt concentration, saving the eluant each time, run then on a coomassie gel and look for a band of the correct weight, when you think you know what salt concentration it elutes at cut out the band/s and sense them for mass spec...
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