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there are a number of different experiments you could do to analyze this. Beads are probably the best and the easiest, but you could also do, for example, an electrophoretic mobility shift assay.
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So if my protein is holding a piece of DNA, it will bind beads that has an affinity to DNA.
And use antibodies to detect it on Western maybe?
Do you have any literature I can look up to get more details?
But you see that I am trying to find whether my protein ever binds to DNA.
Therefore I do not know the target DNA sequence.
I thought I can't do electrophoretic mobility shift assay if I don't know the target sequence.
1. Express protein in question with tag (his tag for example).
2. Purify protein in question and bind it to column through tag (his tag column for example).
3. Isolate total DNA (whatever you want to assay).
4. Add DNA to column containing protein.
5. Wash unbound DNA.
6. Elute protein/DNA mixture - research conditions for binding and washing to make sure not to affect protein-DNA interactions.
7. Proceed with electrophoretic mobility shift assay AND/OR isolate DNA, clone, and sequence.
8. Let us know the outcome.
you can also try putting the protein together with dna, and then denaturing with formaldehyde to make them bind irreversibly then wash away excess dna and then remove formaldehyde. If any dna was bound to the protein, it should come off now.
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Thank you for the suggestion.
I guess the only tricky part will be the preparation of DNA.
To clone it, I will need manageable sizes of DNA so I might have to treat it with DNAse or nucleases.
How much should I add?
For the electrophoretic mobility shift assay, how would I detect it?
Maybe a Western blot?
For DNA prep use kit. Final step should be elution with 50 or 100 ul of water/elution buffer. If you do 100 ul, do it in 2 steps and use 35ul from the 1st elution step for each digestion.
I would suggest to do several (let's say 5-10) 5 and 6 cutter restriction enzyme digestions (done overnight).
For detection you can use either non-denaturing TBE-polyacrylamide gels or TAE-agarose gels - you can also release DNA first and run it on a regular TBE-agarose gel. If sufficient amounts of DNA present, you will be able to visualize with ethidium bromide.
Western is another possibility.
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