RIII, also called β-glycan, is a cell-surface proteoglycan.

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#Unit 13. Methods in Biology

You want to study the potential interaction between nucleosome-bound DNA and a specific histone deacetylase. You decide to perform an electrophoretic mobility shift assay (EMSA).

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#Unit 13. Methods in Biology

Footprinting is a method for detecting protein–DNA interactions that can tell where the target site lies on the DNA and even which bases are involved in protein binding.

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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.