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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.
In vivo footprinting is a technique used to analyze the protein-DNA interactions that are occurring in a cell at a given time point. [5] [9] DNase I can be used as a cleavage agent if the cellular membrane has been permeabilized. However the most common cleavage agent used is UV irradiation because it penetrates the cell membrane without ...
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] These two core sheets run parallel, and all others run antiparallel.
Several studies have employed the use of Hi-C to describe and study chromatin architecture in different cancers and their impact on disease pathogenesis. Kloetgen et al. used in situ Hi-C to study T cell acute lymphoblastic leukemia (T-ALL) and found a TAD fusion event that removed a CTCF insulation site, allowing for the oncogene MYC ’s ...
Deoxyribonuclease I (usually called DNase I), is an endonuclease of the DNase family coded by the human gene DNASE1. [5] DNase I is a nuclease that cleaves DNA preferentially at phosphodiester linkages adjacent to a pyrimidine nucleotide, yielding 5'-phosphate-terminated polynucleotides with a free hydroxyl group on position 3', on average producing tetranucleotides.
At sufficient concentrations, DNase I is capable of digesting nucleosome-bound DNA to 10bp, whereas micrococcal nuclease cannot. [17] Additionally, DNase-seq is used to identify DHSs, which are regions of DNA that are hypersensitive to DNase treatment and are often indicative of regulatory regions (e.g. promoters or enhancers). [57]
Radioactive sulfur-35 was used to label the protein sections of the T2 phage, because sulfur is contained in protein but not DNA. [ 6 ] Hershey and Chase inserted the radioactive elements in the bacteriophages by adding the isotopes to separate media within which bacteria were allowed to grow for 4 hours before bacteriophage introduction.
An electrophoretic mobility shift assay (EMSA) or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein–DNA or protein–RNA interactions. This procedure can determine if a protein or mixture ...