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PRIMA: a rapid and cost-effective genotyping method to detect single-nucleotide differences using probe-induced
Hiroyuki Kakui1,2, Misako Yamazaki1, Kentaro K Shimizu3,4
1Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland.
Scientific Reports
|October 24, 2021
Summary
We developed PRIMA, a novel method for detecting small DNA mutations like 1-base pair insertions/deletions (indels). PRIMA enhances heteroduplex mobility assay (HMA) for rapid, cost-effective genotyping and SNP detection.
Area of Science:
- Molecular Biology
- Genetics
- Biotechnology
Background:
- CRISPR and other nucleases generate 1-base pair (bp) insertion or deletion (indel) mutations.
- Existing methods for detecting 1-bp indels have limitations in cost and/or resolution.
- Traditional Heteroduplex Mobility Assay (HMA) has limited resolution and complex band patterns.
Purpose of the Study:
- To develop a novel, high-resolution method for detecting 1-bp indels.
- To improve upon the limitations of traditional HMA.
- To provide a rapid and cost-effective genotyping solution.
Main Methods:
- Development of PRIMA (Probe-Induced HMA), a modified HMA technique.
- Utilizing a short single-stranded DNA probe with a specific deletion within HMA.
- Testing PRIMA on DNA fragments from plants, bacteria, and humans.
Main Results:
- PRIMA consistently detected 1-bp indel mutations.
- PRIMA demonstrated the ability to detect single nucleotide polymorphisms (SNPs).
- The method proved effective across different species.
Conclusions:
- PRIMA offers a significant advancement in detecting small DNA mutations.
- This method provides a rapid, cost-effective, and high-resolution alternative for genotyping.
- PRIMA has broad applicability in genetic analysis across various organisms.
