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A second pair of primers was used to amplify AtHMA4 cDNA within the region corresponding to the C-terminus of the protein.
Similar experiments were performed with a second pair of primers (LP6 and LP7), which are separated by 486 bp in genomic DNA and flank the GC-rich segment (Figure 3c,d).
This cox1 sequence was then used as a template for designing a second pair of primers (cox1-F; cox1-R).
If amplification with the Primer 3-designed primers did not yield expected products, a second pair of primers was designed using CLC DNA workbench.
These primers produce a product of approximately 1kb for individuals with no deletion, and a second pair of primers was designed that flank the deletion site.
A second pair of primers containing a different selection marker can be similarly prepared so that multiple rounds of 'error-prone PPCP – transformation – selection' process can be conveniently performed over a target gene for directed evolution (Fig. 4).
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A third pair of primers, KanF and rpslR, were used to amplify a 1.3-kb positive/negative selection cassette kan-rpsL + that was previously introduced in S. pneumoniae strain 403 J [ 23].
As the quality of DNA obtained from formalin-fixed paraffin-embedded tumour tissue affects the success rate of MSP, in some cases MGMT methylation status was determined by a different nested-MSP approach, with a first pair of primers to obtain smaller amplicons (129 bp), for which forward and reverse primers have been described (Palmisano et al, 2000; van Engeland et al, 2003).
If the first set of primers failed to amplify, a second pair of PCR primers was designed.
In addition to the standard primers, we designed a second pair of consensus primers with a minimal number of mismatches between chicken and shorebird sequences.
The PCR products were reamplified with a second pair of PCR primers (5'-GACTAGCTTGGTGCCGAATTCGCGGTTAAA-3', 5'-GAGCCAACAGGCACCGAATTCCT CACTAAA-3') for 10 cycles in the same conditions.
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