Plasmalogens are ether glycerophospholipids in which the alkyl moiety is cis-a, b-unsaturated

      

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#Unit 13. Methods in Biology

Several methods are available, but three are very popular: DNase, dimethylsulfate (DMS), and hydroxyl radical footprinting. 

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#Unit 13. Methods in Biology

DNase footprinting relies on the fact that a protein, by binding to DNA, covers the binding site and so protects it from attack by DNase. 

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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.