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Briefly, a first PCR was performed to amplify the 5' and 3' ends of the promoter regions using primers that introduced the desired mutations.
Episomal ChIPs (eChIPs): All regions to be cloned into the episomal vector (with the exception of GMNN which has been described previously in [23] were amplified from Ntera2 genomic DNA by PCR with Pfx Polymerase (Invitrogen) using primers that introduced unique XhoI and HindIII sites immediately 5' and 3' to the region of interest, respectively.
Genes encoding antibiotic resistance were amplified using primers that introduced extra sequences for use in either PCR amplification of selection cassettes or in the genome editing procedure itself.
The mitochondrial-targeting sequence (from atp2-1) wamplifiedied from tobacco using primers that introduced an XbaI site at the 5' end and a BamHI site at the 3' end.
A 1.59-kbp DNA segment bearing the SNP1 gene (nucleotides −400 to +1190) was amplified from S. cerevisiae genomic DNA by PCR using primers that introduced restriction sites for inserting the gene into the yeast expression plasmids pRS316 (CEN URA3 ) and pRS413 (CEN HIS3 ).
The human COL2A1 gene was amplified from IMAGE consortium [ 41] CloneID 7486698 using primers that introduced a 5' BglII restriction site and a 3' BamHI site flanking the gene (forward primer: TTA GAG ATC TAC CAT GAT TCG CCT CGG GGC TCC CCA GAC GCT GG; reverse primer: TAA TCG GAT CCT ATT ACA AGA AGC AGA CCG GCC C).
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To ensure that the gene had been amplified without introducing nucleotide errors, both strands were sequenced using primers that were specific for the T7 and SP6 promoters.
First, the Int-coding sequence (CDS) was amplified in separate reactions as incomplete 5′ and 3′ fragments using primers that hybridized to the ends of the Int CDS paired with internal primers designed to introduce the desired point mutation(s).
cDNA encoding scFv-6E (GenBank accession number FJ695518) was amplified by PCR using complementary primers that introduced a 5' Kozak initiation sequence for mammalian expression and a 3' HA epitope (YPYDVPDYA) for biochemical detection.
NRP1WT, NRP1ΔSEA, and NRP1ΔCyto lentiviruses were based on the NRP1 pcDNA 3.1 construct and generated by PCR using the following primers that introduced NotI and BamHI restriction sites.
The uvrA, uvrB and uvrC coding regions were amplified from E. coli MG1655 genomic DNA using PCR with primers that introduced a BamHI site immediately upstream of the start codon and a HindIII site immediately downstream of the stop codon.
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