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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 agar is used to test whether a microbe can produce the exoenzyme deoxyribonuclease (DNase), which hydrolyzes DNA. Methyl green is used as an indicator in the growth medium because it is a cation that provides an opaqueness to a medium with the presence of negatively charged DNA strands. When DNA is cleaved, the media becomes clear ...
TUNEL is a method for detecting apoptotic DNA fragmentation, widely used to identify and quantify apoptotic cells, or to detect excessive DNA breakage in individual cells. [3] The assay relies on the use of terminal deoxynucleotidyl transferase (TdT), an enzyme that catalyzes attachment of deoxynucleotides, tagged with a fluorochrome or another ...
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.
[32] [33] This technique allows the analysis of protein complexes that bind to DNA (DPI-Recruitment-ELISA) or is suited for automated screening of several nucleotide probes due to its standard ELISA plate formate. [34] [35] DNase footprinting assay can be used to identify the specific sites of binding of a protein to DNA at basepair resolution ...
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 ...
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]