Proximate causes - The subject of cell biology, neurobiology, and many other biological disciplines

Ultimate causes - Their historical causes, especially the action of natural selection

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#Unit 13. Methods in Biology

We perform DNase footprinting by binding the protein to its DNA target, then digesting the DNA–protein complex with DNase. 

When we electrophorese the resulting DNA fragments, the protein binding site shows up as a gap, or “footprint,” in the pattern where the protein protected the 

DNA from degradation.

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#Unit 13. Methods in Biology

Footprinting is a means of finding the target DNA sequence, or binding site, of a DNA-binding protein.

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#Unit 13. Methods in Biology

DNase footprinting gives a good idea of the location of the binding site for the protein, but DNase is a macromolecule and is therefore a rather blunt instrument for probing the fine details of the binding site.

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#Unit 13. Methods in Biology

DNA-binding proteins frequently perturb the DNA within the binding region, distorting the double helix. These perturbations are interesting, but are not generally detected by DNase footprinting because the protein keeps the DNase away.

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#Unit 13. Methods in Biology

More detailed footprinting requires a smaller molecule that can

fit into the nooks and crannies of the DNA–protein complex and reveal more of the subtleties of the interaction. A favorite tool for this job is the methylating agent dimethyl sulfate (DMS).

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#Unit 13. Methods in Biology

DMS footprinting follows a similar principle, except that we use the DNA methylating agent DMS, instead of DNase, to attack the DNA–protein complex.