Technique / Molecular Biology / DNA-protein interactions / DNase I footprinting assay

DNase footprinting assay is used to detect DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage. This makes it possible to locate a protein binding site on a particular DNA molecule.

Long Range Footprinting Protocol (SP1) protocol
This protocol is from Machida lab at Japan National Institute of Bioscience & Human-Technology and is based on Based on Bio-Techniques,23, 300-303 (1997). ...

A modified protocol for in vivo footprinting by ligation-mediated polymerase chain reaction protocol
A free accessible original paper on PCR footprinting. Reference: Nucleic Acids Res. 1994 Feb 11;22(3):532-3 A modified protocol for in vivo footprinting by ligation-mediated polymerase chain reaction. Dimitrova D, Giacca M, Falaschi A. I ...

DNase I Protection protocol
A short protocol on DNase I protection from Molecular Biology of Nuclear Receptors, France. You will have first to determine the concentration of DNaseI that cleaves 30-50% of your input DNA. A rule of thumb is to multiply this amount by 10 to get the adeq ...

Genetic Footprinting Protocol protocol
Detailed protocols for genetic footprinting, a technique for high-resolution mapping of the functional organization of cloned genes (Singh, Crowley and Brown (1997) PNAS 94: 1304-1309). Reference: Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1304-9. Hig ...

Footprinting new review
Footprinting is a method for determining the exact DNA sequence to which a particular DNA-binding protein binds. This brief introduction is from Kimball's Biology Pages. This page also contains a nice illustration on principle of footprinting. ...

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Figure. A gel-mobility shift assay
(Molecular Biology of the Cell)
II. Basic Genetic Mechanisms 7. Control of Gene Expression DNA-Binding Motifs in Gene Regulatory Proteins

Figure. DNase I footprinting, a common technique for identifying protein-binding sites in DNA
(Molecular Cell Biology)
10. Regulation of Transcription Initiation 10.2. Bacterial Transcription Initiation