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A DNase footprinting assay [1] is a DNA footprinting technique from molecular biology/biochemistry that detects 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.
The DNA template labeled at the 3' or 5' end, depending on the location of the binding site(s). Labels that can be used are: radioactivity and fluorescence.Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique.
For example, all of the beers produced by a particular brewery could collectively be referred to as its zymography. [citation needed] See also Zymology or the applied science of zymography. Zymology relates to the biochemical processes of fermentation, especially the selection of fermenting yeast and bacteria in brewing, winemaking, and other ...
The principle behind this test is to use enzymes native to the organism to create a colored product in the presence of foreign molecules. The chemical 5-bromo-4-chloro-3-indolyl-beta-D-galactoside is used in the test because N. lactamica can hydrolyze it with the production of β- galactosidase , turning the solution into a blue color.
DNase I Structure: DNase I is a glycoprotein with a molecular weight of 30,000 Da and a carbohydrate chain of 8-10 residues attached to Asn18 (orange). [3] It is an 𝛼,𝛽-protein with two 6-stranded 𝛽-pleated sheets which form the core of the structure. [ 4 ]
This was the first example of MNase-seq in any organism. It was not until 2008, around the time Next-Generation sequencing was becoming more widely available, when MNase digestion was combined with high-throughput sequencing, namely Solexa/Illumina sequencing , to study nucleosomal positioning at a genome-wide scale in humans. [ 2 ]
Nuclease protection assays are used to map introns and 5' and 3' ends of transcribed gene regions. Quantitative results can be obtained regarding the amount of the target RNA present in the original cellular extract - if the target is a messenger RNA, this can indicate the level of transcription of the gene in the cell.
An antibody that recognizes the protein can be added to this mixture to create an even larger complex with a greater shift. This method is referred to as a supershift assay, and is used to unambiguously identify a protein present in the protein – nucleic acid complex.