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Bisulphite treated DNA is subject to PCR amplification using primers that include T7 RNA promoter sequences.
A method based on the amplification of the entire plasmid using primers that include the desired changes was employed for the site-directed mutagenesis [ 38].
For expression of recombinant proteins, the cDNA or DNA fragments were cloned into pMCSG9 or pMCSG10 vectors to produce His-MBP or His-GST-tagged proteins respectively, by ligation independent cloning (Eschenfeldt et al., 2009) using primers that include 18 nt identical to the ends of the linearized pMCSG vector (Supplementary file 8).
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GFP variants were each amplified from their original pET15 expression vectors (Raghavan et al. 2012) using primers that included restriction sites to enable cloning into the appropriate vector.
To produce the SD10 constructs, gt genomic fragments were PCR-amplified from CH322-101F2 or CH322-5H16 BAcloneses (BACPAC resources: http://www.pacmanfly.org/) using primers that included FRT sequences and NspI sites (Supporting Information, Table S1).
DNA encoding kinase domain residues 672 998 (mature protein numbering), equivalent to residues 696 1022 (precursor protein numbering) of human EGFR (NCBI sequence NP_005219.2) was amplified by PCR using primers that included an N-terminal His6 tag and SpeI/XhoI restriction sites.
Twenty-one full-length NITR cDNAs were cloned from medaka kidney and spleen by 3' RACE using nested primers that include the predicted translational start codon (Additional Files 4 and 5) in order to verify the exon-intron boundaries for the NITRs.
Fragments that include the terminal end of the IS 6110 were then amplified in a nested PCR using primers that incorporate additional barcodes.
Typhimurium LT2 was PCR-amplified using 5' and 3' primers that included KpnI and HindIII sites, respectively.
3′-UTR of NOB1 and a mutation sequence were amplified by PCR using the primers that included a Bgl II restriction site on the 5′ and 3′ strands.
Constitutively active forms of FAK, PI3K, and AKT isoforms were generated by amplification of respective cDNAs using 5′ primers that included c-Src myristoylation signal sequences, followed by cloning into CSII vector.
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