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When creating a targeting cassette specific for a particular gene, it is imperative to amplify from a completely linearized and purified cassette template.
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Allele exchange cassettes specific to target loci were either constructed by SOE PCR [ 45] or commercially synthesised.
The cassette provides a 200-bp sequence, which is used to design a variety of cassette-specific primers.
Integration of the GFP fusion at the PDR5 locus was confirmed by PCR using combinations of primers flanking PDR5 gene and GFP-kanMX6 cassette-specific primers.
The cassette-specific J-C intergenic regions include the sequence spanning from 5' of distal J segment and 3' of C gene (exon 3) for each TRGC cassette.
Plasmid DNA from recombinant clones was isolated from each exon trapping library and sequenced with vector-cassette-specific primers SD2 and SA4 using ABI-Prism BigDye terminator cycle sequencing kit (Applied Biosystems).
Pre-amplification was performed by using an element-specific primer and an cassette-specific primer C1 (TaKaRa) in a final 20 μL volume with 4 pmol of each primer, 1 unit LA Taq DNA polymerase (TaKaRa), 0.2 mM dNTPs and 1 × PCR buffer.
Several hundred colonies were obtained and candidate clones were then screened by PCR for correct integration of the RfA-Destination cassette into pWY189 using the cassette-specific primers Cm-5'-AS1 and C1 in combination with the gene-specific primers PAP85-DEST-Integ-5'-Test and PAP85-DEST-Integ-3'-Test, respectively.
The gene cassette with specific promoters responsive to UV irradiation in pIG121-HmR.
Knockout mutations were verified by PCR amplification of genomic loci expected to contain the 1327 base pair gene replacement cassette with specific primers (Table S4 in Additional file 1).
Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination.
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