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The P-DNA solutions were concentrated to ∼1 mM DNA using an Amicon Ultra-0.5 centrifugal filter unit, 3 kDa (Millipore) and purified using reverse phase HPLC (Agilent 1260 Infinity, DIKMA Inspire C18 column (5 um, 250 × 4.6 mm)) with a gradient of organic buffer B (90% acetonitrile in water, + 50 mM TEAA, pH 7) in water + 50 mM TEAA, pH 7 (buffer A).
Unless otherwise stated, the NMR samples contained 0.5 1 mM DNA oligonucleotide.
All samples for ITC experiments were pre-equilibrated in 50 mM Tris, pH 7.5 containing 50 mM NaCl and 2 mM 2-mercaptoethanol, and 0.5 mM DNA (12 mer or 16 mer, Fig. 1) and titrated with 6 mM DNA in the syringe at 27°C.
Overall, the effect of KCl concentration is similar among the variants: at 20 mM, DNA synthesis is stimulated; at 50 mM, we observe no stimulation and/or slight inhibition; at 100 mM, Hspol γ is inhibited completely.
DNA and protein complexes were assembled using the 563 bp IL2RA DNA fragment in a final volume of 10 µl, with reaction mixture containing 10 mM DNA fragment, 5 µl of binding buffer (10 mM Tris-HCl, pH 7.5, 10 mM MgCl2, 100 mM NaCl, 10% Glycerol).
A 9700 instrument was used to fragment at 37°C for 35 minutes, then 95°C for 15 min. Labeling of target used 30 mM DNA Labeling Reagent, 30 U/μL Terminal Deoxynucleotidyl Transferase, and 5× TdT Buffer (Affymetrix).
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When 10 fM of DNA-t was deposited, it showed a high current value as opposed to 3 mM DNA-t.
The PCR mixture contained 1 × PCR buffer; dATP,dCTP, dGTP,dTTP (2 μM each); primers (100 nM); MgCl2 (1.5 mM); Taq DNA polymer (2 U); and template DNA (200 ng) in a final volume of 50 μL.
At moderate salt concentrations (75 mM) SV40 DNA is cleaved once, most often within either one of the two following regions: the segments defined as 0.15 to 0.25 and 0.45 to 0.55 SV40 fractional length, clockwise, from the EcoR(I) restriction endonuclease cleavage site (defined as the zero position on the SV40 DNA map).
In 9 patients with primary tumors with a Breslow depth greater than 0.75 mm, the DNA content was also determined in nuclei obtained from formalin-fixed paraffin-embedded tissue.
When the cells were transfected with PKCδ, exposure to either etoposide (0.07 µM) or BSO (1 mM) induced DNA fragmentation and oxidation.
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