1. A mixing heteroduplex mobility assay (mHMA) to genotype homozygous mutants with small indels generated by CRISPR-Cas9 nucleases
- Author
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Samantha D. Foster, Ashley N. Turner, Sarah R. Glover, Kiranam Chatti, and Anil K. Challa
- Subjects
Genotyping ,Mixing heteroduplex mobility assay (mHMA) for screening homozygous mutants ,Clinical Biochemistry ,Mutant ,Gene editing ,010501 environmental sciences ,Biology ,01 natural sciences ,Homozygosity ,DNA sequencing ,High Resolution Melt ,03 medical and health sciences ,Genome editing ,Biochemistry, Genetics and Molecular Biology ,HMA ,CRISPR ,Zebrafish ,030304 developmental biology ,0105 earth and related environmental sciences ,Genetics ,0303 health sciences ,Amplicon ,Medical Laboratory Technology ,PCR ,Simple CRISPR-Cas9 ,Heteroduplex - Abstract
Graphical abstract Abstract The development of gene editing technologies, especially the CRISPR-Cas9 system, has been pivotal for understanding the functional role of proteins. Rapid and efficient genotyping methods are necessary to screen for generated mutations and streamline the isolation of homozygotes. CRISPR-Cas9 system targeting a single site in the gene typically results in small indels. Many genotyping methods utilize the heteroduplex that is formed when wild-type and mutant amplicons with small indels anneal during PCR creating a bubble due to mismatched strands. These methods include T7 endonuclease/Cel-I assay, high resolution melting (HRM) analysis, and heteroduplex mobility assay (HMA). Our protocol explains a simple, two step method of a mixing HMA (mHMA) to identify homozygous mutants, a modification of the previously published HMA. We have utilized the mHMA for screening and genotyping numerous CRISPR generated models. The mHMA method to differentiate homozygous wild type from homozygous mutant animals eliminates - • DNA sequencing, even with small indels that can be difficult to discern on a gel. • additional enzymatic reaction steps, such as with the T7EI/Cel-I assay. • specialized equipment and analysis tools, such as with HRM analysis.
- Published
- 2019
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