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First, the VH PCR products were cloned to pHAL14 as described [35], [34], [61] followed by a second cloning step to insert the VL PCR fragments.
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The vector for protein production, pJB-GST-HTS-HS-GFP, was created by first cloning a 7 amino acid spacer fragment containing an XhoI site into pET-15b (Novagen) using sticky ligation and BamHI/XhoI sites.
Y. pestis strains overexpressing one of each of the ten GGDEF/EAL/HD-GYP genes (Table 1) were made by first cloning a wild-type copy of each gene, PCR-amplified from KIM6+ using specific primers, into the high-copy number plasmids pUC18 or pCR2.1-TOPO (Invitrogen).
HA GPC6 was constructed by first cloning an in-frame HA epitope tag between the signal sequence and the coding region of GPC6.
A miRNA expression vector was constructed by first cloning the human Pol II U1 promoter upstream of a multiple cloning site in the Bluescript SK plasmid to create SK-U1.
In the second cloning step, the resulting intermediate plasmid is opened at two positions by a second BsmBI digestion at the cloning sites within Insert-1, and a second DNA fragment "Insert-2" is inserted by conventional ligation, in the process removing both BsmBI sites (Fig. 1d).
pAMW-dMFN, pAGW-dMFN and pTMW-dMFN were generated by first cloning dMFN cDNA (DGRC-RE04414) into pENTR-3C and then performing a recombination reaction into pAMW (actin promoter with N-terminal Myc tag), pAGW (actin promoter with N-terminal GFP tag) and pTMW (pUAST vector with N-terminal Myc tag).
Briefly, probes for detecting rat CnAß-FK mRNA were prepared by first cloning the full sequence of intron 11 of CnAß-FK cDNA (Figure 2A) into pCR-Blunt II-TOPO (Invitrogen).
Synthetic operons were constructed by first cloning into pHB201 then transferring to pHCMC04G resulting in eight different pHCMC04G constructs.
pCDNA3-Flag-Reaper and deletion mutants were generated by first cloning Reaper cDNA or mutants into pENTR-3C (Invitrogen Corp., Carlsbad, CA, USA).
Substrates for Tev-mTALENs were constructed by first cloning oligonucleotides corresponding to the target site into the XbaI/SphI sites of pTox.
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