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Upon sequencing a single colony for each mutagenesis reaction, coverage of 80 90% of the targeted Sav mutants was achieved after PCR and transformation in E. coli TOP10.
DNA sequencing showed that in each mutagenesis reaction all four transformants contained the desired mutations.
A volume of 7.5 µl for each mutagenesis reaction was used to transform 50 µl DH5α cells (New England Biolabs).
Sequence analysis the plasmid DNA revealed that in each mutagenesis reaction all four transformants contained the desired mutations or deletions.
The correct integration of each mutagenesis cassette was verified by PCR screening using diagnostic primers located upstream and downstream of the target sites.
SrEpac was generated through serial clonal isolation to ensure a genetically homogeneous background for the screen, and frozen stocks of SrEpac were thawed prior to each mutagenesis to limit the accumulation of random mutations.
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Primers for each respective mutagenesis were designed using Stratagene's web-based QuickChange® primer design program http://www.stratagene.com/qcprimerdesigne (primer sequences are found in Additional file 1; Table S1).
To map functional ESEs we introduced 34 30-nt microdeletions of the 5' and 3' ends of each exon by mutagenesis, two on each exon end that overlapped 5 nucleotides, except for the final exon 27 where only two deletions were made on its 5' end.
The structures show that two MADS domains extensively contact each other, but mutagenesis data indicate that also other parts of the MIKC proteins contact each other.
Each round of mutagenesis was confirmed by sequencing.
Listed below are steps followed for each generation of mutagenesis with slight variations based on the screening plate used in first step of selection.
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