A rapid and cost-effective Chelex-100 resin-based method for genomic DNA extraction from adult zebrafish tissues
- 1School of Basic Medicine and Forensic Medicine, Henan University of Science and Technology, Luoyang, China
- 2Institute of Special Medicine, Henan University of Science and Technology, Luoyang, China
- 3Forensic Center, Henan University of Science and Technology, Luoyang, China
Abstract
The zebrafish (Danio rerio) is a widely used vertebrate model in biomedical research, yet the rapid and cost-effective extraction of genomic DNA (gDNA) from adult zebrafish tissue remains a practical challenge for routine molecular applications. To address this, we systematically optimized and evaluated a Chelex-100/proteinase K-based extraction protocol across eight adult zebrafish tissues (muscle, liver, heart, spleen, kidney, intestine, brain, and eggs) and compared its performance against that of a commercial kit. The optimized protocol, involving incubation at 56 °C for 15 min and boiling at 100 °C for 10 min, required approximately 25 min per sample. Across all tested tissues (3 biological replicates per tissue), the Chelex-100 method yielded gDNA concentrations ranging from 177.2 ± 3.5 ng/µL to 674.5 ± 22.1 ng/µL per 5 mg of tissue, which were generally higher than those obtained with the commercial kit. However, the purity (A260/A280 ratios) was consistently lower for the Chelex-100 method (1.36–1.83) than for the kit (1.84–2.02), indicating the coextraction of proteinaceous impurities. Despite this, Chelex-extracted gDNA supported successful PCR amplification and Sanger sequencing of target fragments, with consistent amplicon quality. In real-time PCR assays, both methods produced amplification curves, but the Chelex-100 method yielded systematically higher Ct values, suggesting reduced sensitivity with less-pure templates. Crucially, the Chelex-100 method avoided hazardous organic solvents and required no column purification, with an estimated reagent cost of <$0.20 per sample versus approximately $2.00 per sample for the commercial kit. We conclude that this optimized Chelex-100/proteinase K protocol provides a rapid, economical, and operationally simple alternative for routine gDNA extraction from adult zebrafish tissues and is particularly suitable for PCR-based genotyping, sequencing and qPCR applications, though its lower purity warrants careful consideration for high-sensitivity quantitative assays.
Related
- Persistence of viral full-length genomic RNA and replication-associated RNA transcripts and proteins in sheep tissues following acute Crimean-Congo hemorrhagic fever virus infection
- Time-dependent changes in dental and alveolar tissues in kidney disease
- The effect of retinoic acid on visual function and ocular tissues in guinea pigs with form-deprivation myopia
- Multi-modal spatial glycomic analysis of lymphoid aggregates in prostate and pancreatic cancer tissues
- Effects of Photoaged Polyethylene Microplastics on Cardiac Injury and Fibrosis-like Remodeling in Zebrafish
BibTeX
@article{feng2026rapid,
title = {{A rapid and cost-effective Chelex-100 resin-based method for genomic DNA extraction from adult zebrafish tissues}},
author = {Wei Feng and Boya Li and Yiqiong Niu and Qiannan Xu and Xiandun Zhai},
journal = {PLOS One},
year = {2026},
month = sep,
doi = {10.1371/journal.pone.0358591},
url = {https://doi.org/10.1371/journal.pone.0358591},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A rapid and cost-effective Chelex-100 resin-based method for genomic DNA extraction from adult zebrafish tissues
AU - Wei Feng
AU - Boya Li
AU - Yiqiong Niu
AU - Qiannan Xu
AU - Xiandun Zhai
PY - 2026
DA - 2026/09/18
JO - PLOS One
DO - 10.1371/journal.pone.0358591
UR - https://doi.org/10.1371/journal.pone.0358591
AB - The zebrafish (Danio rerio) is a widely used vertebrate model in biomedical research, yet the rapid and cost-effective extraction of genomic DNA (gDNA) from adult zebrafish tissue remains a practical challenge for routine molecular applications. To address this, we systematically optimized and evaluated a Chelex-100/proteinase K-based extraction protocol across eight adult zebrafish tissues (muscle, liver, heart, spleen, kidney, intestine, brain, and eggs) and compared its performance against that of a commercial kit. The optimized protocol, involving incubation at 56 °C for 15 min and boiling at 100 °C for 10 min, required approximately 25 min per sample. Across all tested tissues (3 biological replicates per tissue), the Chelex-100 method yielded gDNA concentrations ranging from 177.2 ± 3.5 ng/µL to 674.5 ± 22.1 ng/µL per 5 mg of tissue, which were generally higher than those obtained with the commercial kit. However, the purity (A260/A280 ratios) was consistently lower for the Chelex-100 method (1.36–1.83) than for the kit (1.84–2.02), indicating the coextraction of proteinaceous impurities. Despite this, Chelex-extracted gDNA supported successful PCR amplification and Sanger sequencing of target fragments, with consistent amplicon quality. In real-time PCR assays, both methods produced amplification curves, but the Chelex-100 method yielded systematically higher Ct values, suggesting reduced sensitivity with less-pure templates. Crucially, the Chelex-100 method avoided hazardous organic solvents and required no column purification, with an estimated reagent cost of <$0.20 per sample versus approximately $2.00 per sample for the commercial kit. We conclude that this optimized Chelex-100/proteinase K protocol provides a rapid, economical, and operationally simple alternative for routine gDNA extraction from adult zebrafish tissues and is particularly suitable for PCR-based genotyping, sequencing and qPCR applications, though its lower purity warrants careful consideration for high-sensitivity quantitative assays.
SN - 1932-6203
ER -