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PMB is capable of recognizing target DNA and serves as signal reporter, while PPT is designed to harbor the half binding site of nicking endonuclease and is used as the primary polymerization primer.
Only genes containing both a potential core binding site and a potential half binding site were considered as positive for the presence of a "complete QRE".
After potential core sites were identified, neighboring sequences both upstream and downstream of these potential sites were searched for the presence of a potential half binding sites using a second weighted matrix.
To that end, we used the ConTra matrix (Hooghe et al, 2008) and found two GRE elements and one GR half binding site (Fig 5D).
As shown in Figure 6A, binding of [H]-BH4 appears to display two phases with about half of the label bound within seconds, and the other half binding with apparent rate constants of 0.91 ± 0.16, 0.55 ± 0.10, and 0.076 ± 0.006 min–1 at 37, 25, and 8 °C, respectively.
The software identifies possible sites using parameters based on a previously described protocol (Cermak et al., 2011): the length of the target sequences for each TAL-binding domain (half binding domains, either on the right or left of the cutting site) was set to be between 15 and 20 bp.
Similar(54)
It is possible that a similar intramolecular interaction occurs in HKIII, and reduction in N-half glucose binding results in diminished C-half binding, and an overall reduction in activity; however, other possibilities cannot be excluded.
Specifically, ERs that work through Sp1 or AP1 sites would not be detected by this assay, nor would EREs with half-binding sites only.
By introducing two mutations in the T-box half-binding site of the p21 promoter reporter vector ('mutated p21 promoter' Figure 7a), it was demonstrated that binding of Brachyury is required for repression of p21 transcriptional activity, because mutation of the T-box half-binding site enhanced the transcriptional activity of the p21 promoter in H460 control.shRNA cells.
Univalent A33scFv showed about half the binding activity of divalent of huA33 IgG, and A33scFv CD had slightly less binding activity than A33scFv.
Half maximal binding of peptide-free DR1 to MEM-264 was observed at 5.3 nM, whereas no binding was observed for peptide-loaded DR1 at concentrations up to 2 µM.
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