Deoxyribonuclease I (DNase I) protection mapping, or footprinting, is a valuable technique for locating the specific binding sites of proteins on DNA. The basis of this assay is that bound protein protects the phosphodiester backbone of DNA from DNase I-catalyzed hydrolysis. Binding sites are ...
In particular, we have selected the advanced genome-wide phylogenetic footprinting function (i.e., “searchPairBSgenome” in R) to improve the scanning performance by chaining the human genome (GRCh37) over the mouse genome (mm10), taking advantage of evolutionary conservation (Wasserman and ...
Structure of Anthramycin only possible site left [25). DNA footprinting experiments indicate anthramycin binds to 5'PuGPu sequences over 5'PyGPy sequences [27,28]. The mode of action of anthramycin has been extensively studied. The rate-determining step of anthramycin binding to DNA is a ...
Sample number and characteristics, as well as the desired accuracy, coverage and resolution, influence the choice of technique. DNA methylation is usually measured on a β-distributed absolute scale from 0 to 1, or 0 to 100%, rather than on an infinite scale of log ratios. The unique data...
Materials References Automatic Translation Kaeppel, C., et al.A largely random AAV integration profile after LPLD gene therapy.Nature medicine.19, 889-891 (2013). Voigt, K., et al.Retargeting sleeping beauty transposon insertions by engineered zinc finger DNA-binding domains.Mol Ther.20, 1852-18...
We proceeded to analyse the regions highlighted by DNase I footprinting using electrophoretic mobility shift assays (EMSAs). A radiolabelled probe spanning the region of protection LTB1 showed strong constitutive binding of at least two protein–DNA complexes, which appeared specific on competition with...
It is not, however, possible to ascertain from genomic footprinting what proteins actually arrive at origins as cells exit from mitosis. Using formaldehyde cross-linking (Strahl-Bolsinger et al. 1997), we have measured the association of ORC, Cdc6p, and an Mcm protein with specific DNA ...
IRspectroscopyabstractElectrochemicalDNAbiosensorwasusedtostudytheinteractionofmethotrexate(MTX)withDNAimmobilizedonthebaresurfaceofglassycarbonelectrode(GCE).ThebindingmechanismofMTXwithDNAwaselucidatedbyusingconstantcurrentpotentiometrictechniquefurthersupportedbyUV–VisibleandFT-IRstudies.Thedecreaseinguaninepeakareawasused...
(II) or some pH-dependence of the cleavage reaction. Based on known EDTA cleavage chemistry, it is anticipated that at slightly acidic pH-values, DNA-EDTA-Fe(II) probes do not produce efficient cleavage. In data not shown, footprinting experiments confirm that the triple helix is forming at...
Our current understanding of the expression of eukaryotic class III genes has benefited greatly from studies of the developmentally regulated 5S RNA gene system of the African clawed frog Xenopus (Wolffe and Brown 1988). In addition, how the 5S-specific