One of the most extensively characterized of these factors is PIF3, a basic helix-loophelix (bHLH) transcription factor that interacts with both phyA and phyB.

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#Unit 13. Methods in Biology

A gel mobility shift assay, is a method for detecting DNA–protein interaction relies on the fact that a small DNA has a much higher mobility in gel electrophoresis than the same DNA does when it is bound to a protein. 

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#Unit 13. Methods in Biology

Lane 3 depicts the behavior of the same DNA bound to two proteins. The mobility is reduced still further because of the greater mass of protein clinging to the DNA. This is 

called a supershift. 

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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.