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The avidity of VLP-A was increased by adding a glycine spacer between the C-terminus of the PapMV CP and the peptide, and improved even further by using a duplicated A peptide in the fusion protein.
The DNA/protein cross linking reaction was stopped by adding a glycine stop-fix solution.
To increase the number of identified PrSMs with one PTM, a mutated ST protein database was generated by adding a glycine residue to the middle of each protein sequence in the ST proteome.
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Briefly, cells were cross-linked by adding a final concentration of 1% formaldehyde for 10 min at room temperature and cross-linking was stopped by adding glycine to a final concentration of 125 mM.
CSF regeneration was induced by adding an equal volume of 1 M NaCl and 10 mM glycine, pH 2, followed by one injection of borate, pH 8.5.
Cross-linking was terminated by adding glycine to a final concentration of 125 mM.
Crosslinking was stopped by adding glycine to a final concentration of 0.125M and rotating at RT for 5 minutes.
Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature on a rocking platform.
Incubations lasted for only 8 min to avoid excessive cross-linking and were stopped by adding glycine to a final concentration of 0.15 M. Cell lysates were sonicated to generate 300- to 1,500-base-pair DNA fragments.
In brief, the PHA-treated PBL were suspended in RPMI 1640 medium containing 1% formaldehyde (106 cells/ml), and incubated at 37°C for 10 min. The crosslinking reaction was stopped by adding glycine to a final concentration of 0.125 M and the cells were collected by centrifugation.
Cells were cross-linked with 1% formaldehyde for 3 minutes at 22°C, and reactions were quenched by adding glycine to a final concentration of 0.125 M. Cells were then rinsed in PBS and scraped in ice-cold MNase NP-40 Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 0.15 mM spermine, 0.5 mM spermidine).
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