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Dashed lines indicate the CA values of bare Al2O3 (green) and SiO2/Si (red) substrates.
Therefore, we proceeded to test red-shifted APE1 substrates (hereafter referred to as "red" substrates) by utilizing a combination of carboxytetramethyl rhodamine (i.e. TAMRA) as the fluorophore donor and BHQ-2 [26] as the matching quencher.
Next, the sections were incubated with fast red substrates (Sigma Aldrich, UK) for 10 minutes and counterstained with Carazzi's haematoxylin (Section Lab, Japan) for 2 minutes.
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Sections were then stained for: (a) AP activity [fast red substrate with tetramethylrhodamine isothiocyanate (TRITC) filter; Chroma 49005 ET], and (b) hematoxylin imaging (Zeiss AxioCamMRc 5 color camera).
Alkaline phosphatase activity was revealed using the Vector red substrate (Vector Laboratories).
Visualization of NP was achieved by incubation with streptavidin-alkaline phosphatase and naphthol-fast red substrate (DAKO).
Since we had the ability to modify the nucleotide sequence at will, we designed and tested several variations of the THF-containing red substrate to identify the optimal arrangement for the screening assay.
As another means of probing the selectivity of the candidate APE1 inhibitors (Figure 3), we miniaturized to a 1536-well format a qHTS assay for E. coli EndoIV [19] utilizing the same THF-containing red substrate as above (Figure S3).
During initial optimization, 50 nM of the unlabeled version of the red substrate (Figure 1) was titrated with ThO in 40 µL in 384-well format; 250 nM ThO was selected for subsequent tests.
As evident from Figure 1B, the red substrate exhibited near-identical cleavage kinetics with APE1, but provided an approximately twofold better signal increase, in comparison with the green version.
Sections were treated with anti-CD3 followed by alkaline phosphatase and Vector red substrate.
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