| Assay Method Information | |
| | Enzyme Inhibition Assay: E. coli Topo IV Decatenation |
| Description: | E. coli topoisomerase IV decatenation activity and its inhibition was assayed using a kit procured from Inpiralis (D4002) and the kit protocol was adapted with necessary modifications similar to the gyrase supercoiling assays. The compounds 1, 2, 3 and 4 were incubated individually for 10 minutes with 5 nM of E. coli topoisomerase IV in a 30 μl reaction volume and 3.2% DMSO. The reactions were started with the addition of 60 ng of kDNA and continued for 40 min at 37° C. The final reaction mixture contained 40 mM Tris-HCl (pH 7.6), 100 mM potassium glutamate, 10 mM magnesium acetate, 10 mM DTT, 1 mM ATP, and 50 μg/ml albumin. The reactions were stopped by addition of 0.75 μL of Proteinase K (20 mg/mL) and 3 μL of 2% SDS and further incubated at 37° C. for 30 min. This was followed by the addition of 4 μL of STEB (40% (w/v) sucrose, 100 mM Tris-HCl pH8, 1 mM EDTA, 0.5 mg/ml Bromophenol Blue) and the kDNA/minicircles forms were separated by agarose gel electrophoresis. The 1% agarose gels were run for 3 h at 4V/cm in 1×TAE (40 mM Tris, 20 mM Acetic acid, 1 mM EDTA). To visualize the DNA, the gels were stained for 10 min with 0.7 μg/mL ethidium bromide and excess dye was removed by several washes with water. IC50 values were determined by quantifying the Kinetoplast DNA band inside the gel well and decatenated minicircles that migrate into the gel in each of the reactions from a gel image by a densitometric method using the Quantity One Software (Bio-rad). |
| Affinity data for this assay | |
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