ArticleMolecular and cellular probes2004
Selection for 3' end triplets for polymerase chain reaction primers.
Article in Molecular and cellular probes, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed.
- Limited resolution of DNA barcodes and environmental influence on phytochemical diversity in Berberis integerrima (Berberidaceae).Scientific reports · 2026Article
- PRIMEval: Optimization and screening of multiplex oligonucleotide assays.Scientific reports · 2019Article
- Improved 18S small subunit rDNA primers for problematic nematode amplification.Journal of nematology · 2018Article
- Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species.PloS one · 2010Article
- Predicting failure rate of PCR in large genomes.Nucleic acids research · 2008Article
- Selection for 3'-end triplets for polymerase chain reaction primers.Methods in molecular biology (Clifton, N.J.) · 2007Review
- GENOMEMASKER package for designing unique genomic PCR primers.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 3' end of a primer is a key component of PCR primer design. Many recommendations for the composition and sequence of the 3' end have been suggested based on theoretical considerations, but have not been verified experimentally. We analyzed 3' end triplets of PCR primer sequences obtained from refereed journal articles, to test those recommendations and to make empirical recommendations for primer design. The frequencies of the 64 possible 3'end triplets among 2137 PCR primers from the VirOligo database were not uniformly distributed. From the analysis, we found that unfavored and preferred 3' end triplets existed, and that the apparent preferences were not due to base compositions in viral genome sequences. Comparison of the sequences preferred by practitioners to those recommended, suggested that no single recommendation is entirely satisfactory. We suggest that recommendations be replaced with a scoring system incorporating empirical frequencies such as those reported here.
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Registered trials
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