ArticleNucleic acids research2014
Exquisite allele discrimination by toehold hairpin primers.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 9 citations in OpenAlex.
- Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers.Analytical and bioanalytical chemistry · 2023Article
- Custom selenoprotein production enabled by laboratory evolution of recoded bacterial strains.Nature biotechnology · 2018Article
- Direct nucleic acid analysis of mosquitoes for high fidelity species identification and detection of Wolbachia using a cellphone.PLoS neglected tropical diseases · 2018Article
- Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA.Scientific reports · 2015Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a 'yes/no' answer.
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Registered trials
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