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We sequenced both strands of the PCR product using the original amplification primers and multiple internal primers.
In addition, LT-PCR amplification and sequencing with multiple internal primers verified an ambiguous site in CR1 of red-footed booby individual rf_CocD7, and re-sequencing of a subset of individuals with ambiguities verified our original results.
It appears likely that pPolB, which, by definition, starts DNA replication at the end of the genome, cannot ensure efficient replication of genomes above a certain threshold (probably about 45 kb, as in adenoviruses), owing to the lack of a dedicated primase that would make multiple internal primers along the genome to ensure the completion of lagging strand synthesis.
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In addition to sequence analysis of each deletion, we verified that the deleted sequences had not inserted elsewhere in the genome using multiple sets of internal primers for each deletion (supplementary material Fig. S2).
Because the DNA fragments of each gene contained multiple exons and introns, additional internal primers were used for sequencing of four genes (CPS1, KS1, KO2 and KAO) that were about 2 kb in length.
29 clones were sequenced using vector primers and internal primers Bov 9 and Bov 1146.
In another reaction, forward and reverse Clost primers were used using the conditions for Firm internal primers.
The entire mitogenomes were amplified and sequenced by primer walking using newly designed specific internal primers.
For site-directed mutagenesis of ptmU4, the ptmU4 gene from pBS12092 was amplified in two steps by primer extension44 using the 739StrU4_F and 739Stru4_R primers with internal primers containing the desired mutation.
The PCR product was cloned and sequenced using the forward, reverse and internal primers.
(DOCX 12 KB) 12284_2013_75_MOESM2_ESM.doc Additional file 2: Table S2: Primer combinations used to amplify the Waxy alleles and internal primers used for amplicons sequencing.
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