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Failure of sufficient amplification in wild samples may be due to mutations in primer binding regions.
Although we could not rule out that the absence of amplification of STE3.A1 alleles was due to mutations in primer target sequences, we deem this explanation less likely in this case, since STE3.A1 alleles were identified and sequenced in closely related species of clade B, like R. azoricum and Rh.
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Such high genome heterozygosity can result in a high frequency of null alleles, i.e. alleles fail to amplify due to random mutations in primer-binding regions.
Degenerate and barcode primers failed to amplify reliably across several sample localities in preliminary experiments with polymerase chain reaction (PCR), potentially because of mutations in primer-binding sites for this taxon.
To determine whether amplification failure caused by mutations in primer-binding regions or by complete deletions of the VNTR region were the reason for these null alleles or the insertion of fragments such as mobile genetic elements resulted in larger (and therefore by capillary electrophoresis) undetectable fragments, the respective fragments were analyzed by using standard gel electrophoresis.
The reason could be the presence of novel arsenite oxidase gene within them (Sultana et al. 2012) or mutation in primer binding sites (divergence in its conserved catalytic domain) of the isolates.
KH developed the PRT4 assay and screened the mutation in primer binding site.
We expected to see mutations that arise from two sources: mutations in the primer sequence likely originated during primer synthesis, while those that were found in the ORF were most likely due to PCR-induced errors.
Two samples that had positive results by consensus primers had negative results by the new primers: sample 22 had many mutations in the primer binding site, whereas sample 40 had few mutations.
We deduced that the more DNA (1 ng or 10 ng compared to 0.1 ng) must be used in PCR for detection of HAmo SINE may result from the mutation in primer-matched regions of HAmo sequences in the investigated species since the investigated species diverged more with cyprinids.
Further, mutations in the primer target region may negate the effectiveness of primers.
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