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Forward and reverse strands were re-suspended in duplex buffer (30 mM Hepes [pH 8.0], 100 mM potassium acetate) to a concentration of 100 μM.
To anneal the linkers, 510 μL of 40 μM Oligo_1 and 490 μL of 40 μM Oligo_2 were combined with 250 μL of 5X Duplex Buffer (100 mM Tris HCl pH 8.0, 0.1 mM EDTA, 250 mM NaCl, 25 mM β-mercaptoethanol) and aliquoted into 100 μL in PCR tubes.
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Briefly, 2 nmoles of siRNA was reconstituted in 200 μl duplex resuspension buffer (IDT).
The 1D exchangeable proton spectrum (10.8 13.8 ppm) of the 14 S-DB[ a, l]P-dG 11/11-mer duplex in H2O buffer (pH 6.8), recorded at 500 MHz and 10 °C, is shown in Figure 6A.
The sixth-root R factor (Rx) was calculated by CORMA to evaluate the best representative structure derived from the restrained MD simulation The one-dimensional (1D) exchangeable proton spectrum (10.5 13.8 ppm) of the 14 S-DB[ a, l]P-dG·Del 11/10-mer 11/10-mer H2O buffer (pH 6.8) at 15 °C is shown in Figure 2A.
We also tested the cleavage of duplex 1/8 in buffers containing various organic catalysts.
Formation of the duplex precursor in buffers containing TMACl, which does not facilitate quadruplex formation[43], is observed clearly and reproducibly in our experiments using 0.01 TMgTB.
The cell (Starna, Atascadero, CA) contained 1 nM DNA duplex in the buffers listed below.
F.S. cDNA-RNA duplexes in hybridization buffer were denatured at 98° for 3 minutes and then allowed to hybridize at 70°C for 5 hours.
Varying concentrations of enzyme (0 100 μM) were incubated with 50 nM duplex DNA in reaction buffer for 10 min at 25 °C.
The performance of NCBs was evaluated by comparing their bulk enhancement ratios, which are defined as ER = (Iactivated – Ibuffer)/(Iinactivated – Ibuffer), where Iactivated, Ibuffer, and Iinactivated are the integrated fluorescence intensities of the activated NCB (i.e., the duplex), the sodium phosphate buffer, and the inactivated NCB (i.e., NC probe only), respectively.
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