OddCAPS: a simple, low-cost, universal technique for detecting single nucleotide variants
- 1Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University , Bunkyo-ku, Tokyo 112-8681 ,
- 2Division of Material and Biological Sciences, Graduate School of Science, Japan Women’s University , Bunkyo-ku, Tokyo 112-8681 ,
Abstract
Derived cleaved amplified polymorphic sequence (dCAPS) assays are widely used to detect nucleotide variants, but suitable target sites are often limited because primer designs must preserve PCR amplification while creating restriction enzyme recognition sites. Here we report one-step dual-primer dCAPS PCR (OddCAPS), a modification that uses three primers in a single PCR amplification to overcome this constraint. An intermediate primer and a dCAPS primer sequentially introduce 1–2 base substitutions each, enabling up to four engineered base changes near the nucleotide of interest. By using the intermediate primer at 1/10–1/100 the concentration of the other primers, the desired product is generated directly in a single-tube, one-step PCR. Increasing the number of engineered substitutions improves the chance of using a researcher’s preferred restriction enzyme. In principle, a set of eight common restriction enzymes is sufficient to detect any single-nucleotide variant in any biological or synthetic DNA sequence with this approach.
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BibTeX
@article{kawaguchi2026oddcaps,
title = {{OddCAPS: a simple, low-cost, universal technique for detecting single nucleotide variants}},
author = {Karin Kawaguchi and Yuzuha Komachiya and Mai Muto and Ryoka Teshima and Naoko Sakai and Hayao Ohno},
journal = {G3: Genes, Genomes, Genetics},
year = {2026},
month = oct,
doi = {10.1093/g3journal/jkag303},
url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag303/9002699},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - OddCAPS: a simple, low-cost, universal technique for detecting single nucleotide variants
AU - Karin Kawaguchi
AU - Yuzuha Komachiya
AU - Mai Muto
AU - Ryoka Teshima
AU - Naoko Sakai
AU - Hayao Ohno
PY - 2026
DA - 2026/10/27
JO - G3: Genes, Genomes, Genetics
DO - 10.1093/g3journal/jkag303
UR - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag303/9002699
AB - Derived cleaved amplified polymorphic sequence (dCAPS) assays are widely used to detect nucleotide variants, but suitable target sites are often limited because primer designs must preserve PCR amplification while creating restriction enzyme recognition sites. Here we report one-step dual-primer dCAPS PCR (OddCAPS), a modification that uses three primers in a single PCR amplification to overcome this constraint. An intermediate primer and a dCAPS primer sequentially introduce 1–2 base substitutions each, enabling up to four engineered base changes near the nucleotide of interest. By using the intermediate primer at 1/10–1/100 the concentration of the other primers, the desired product is generated directly in a single-tube, one-step PCR. Increasing the number of engineered substitutions improves the chance of using a researcher’s preferred restriction enzyme. In principle, a set of eight common restriction enzymes is sufficient to detect any single-nucleotide variant in any biological or synthetic DNA sequence with this approach.
SN - 2160-1836
ER -