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A 'one-sided' PCR was performed using 5′-AGGCTGCATTGAGGC-3′ (Common L primer) and a universal amplification primer that binds to the 3′ end of the cDNA.
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Although each dimer may be generated at a low level, they can be amplified together during the subsequent universal amplification to a level that severely hinders the amplification of target amplicons.
The cDNA was used in a second strand synthesis reaction, and universal amplification reaction involving the incorporation of a fluorescent marker.
Each of the putative barcodes derived from the seven coding loci represents a subset of the gene that exhibited the highest level of sequence variation and universal amplification within an easily sequenced read length (<700 bp).
As all complete threads share common universal amplification handles, they can be amplified in a concerted fashion with a single primer pair, one being 6FAM labeled hence allowing for detection after fragment separation using capillary gel electrophoresis.
The purified products were parallel-amplified with a single primer pair, taking advantage of the universal amplification handles present at the ends of all DNA threads.
Even if a number of 'nearly universal' nSCGs are eventually identified in angiosperms, universal amplification and sequencing primers that can be used in an arbitrarily chosen lineage are perhaps less likely to exist than for chloroplast genes due to the relatively rapid underlying substitution rates for nuclear genes.
The enhanced variability of nuclear loci compared to other markers provides great potential, but limits the likelihood of identifying universal amplification primers that will function across a wide taxonomic range.
A 550 600 bp subset of the rbcL molecule (termed rbcL-a) located at the 5' end of the large subunit that exhibited maximal sequence variation and universal amplification was also included in the analysis.
Primary PCR products were re-amplified using an exon 2 upstream nested primer, 2exonR-2381 (5'-CAGGTAGCCGGCATTGGTCTG), and the abridged universal amplification primer.
PCR products were re-amplified in a nested PCR using gene-specific primer 3 (GSP3, Online Resource 3) and the abridged universal amplification primer (AUAP) provided by the kit.
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