How to perform DNA\ase I footprinting?

01 January 2014 1 4K Report

Can anybody answer my question? You have determined the DNA-binding site of a protein by DNA footprinting after labeling one strand. To check your results, you repeat the experiment after labeling the other strand of the duplex. You find that the footprints are slightly offset from one another relative to the sequence of the DNA. If the protein binds to the same duplex in both cases, how can the footprints on the two strands be different?

Steven Chaulk

the protein is not binding straight across the helix, this I would guess to be more typical than atypical

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