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The purification was simply performed by passing the water diluted reaction mixture through neutral Al and QMA cartridges.
The transcripts were incubated in the extracts under splicing conditions, and the complexes formed were captured from diluted reaction mixtures on streptavidin-treated silica slides.
Positive control samples were synthesized by in vitro methylation, using a nuclease-free water diluted reaction mix of 16.5 μl, including an all bird pool of 1 μg DNA, 2 μl 10× NEBuffer2, 2 μl SAM (640 μM), 1 μl SssI methylase (4 U/μl) (New England BioLabs Inc).
The RT reactions were diluted 1 25, and 2 5 µl of diluted reaction was used for quantitative PCR using the 2× polymerase mix (Applied Biosystem) in a 25 µl reaction, with 1 µl of 5 mM of each primers.
Finally, the entire reaction was diluted fivefold in 1X EPB and the diluted reaction was delivered into the polyethylene glycol-, biotin-polyethylene glycol-, and streptavidin-derivatized quartz microfluidic observation flowcell (Blanchard et al., 2004).
When this final aggregation reaction is diluted to reduce the concentration of monomer and the diluted reaction is further incubated, the monomer concentration increases as fibrils dissociate (red square), until equilibrium is reestablished, also after a period of about one month.
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Serially diluted reactions were visualized with 1 mM malachite green and quantified by absorbance at 620 nM using the M1000 Pro plate reader (Tecan).
Briefly, 5 × 100 μL reactions were performed in 1XHF Phusion Polymerase buffer containing 150 μM dNTP, 2U Phusion polymerase, 1 μM terminal oligonucletides as priming agents, and 3 μL of the diluted reassembly reaction per 100 μL reaction.
Before the enzymatic assay, Sac1 proteins from −80 °C storage were first diluted with reaction buffer to make an enzyme reaction stock (0.1 mg/mL or 1.8 μM).
Each reaction consisted of 0.665 µl of product from the diluted RT reaction, 1× TaqMan® Universal PCR Master Mix, 0.5 µl 20× TaqMan® Small RNA Assay and sterile water.
The reaction was stopped by adding 10 μl of o-phenanthroline in 50% p-dioxane diluted with reaction buffer.
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