Abstract
The presence of approximately 200-bp cell-free DNA (cfDNA) in the urine has attracted attention as a biomarker for liquid biopsy. However, it is currently useful only for diagnoses of cancers in which a large amount of cfDNA is excreted in the urine. Therefore, the development of an efficient method for extracting cfDNA existing in small amounts in the urine is essential for diagnosing many other diseases. We examined the effect of particle size, small pore size (surface area), and surface modification of porous silica particles on the efficiency of DNA extraction. Our observations suggested that cfDNA could be captured by tertiary amine–modified particles and then removed from the particles by repeatedly washing with sodium bicarbonate (pH 11). Using this method with 30 mg of triamine-modified particles, we succeeded in extracting a few hundred nanograms of cfDNA from 15 mL urine. Furthermore, we could detect ~ 67 fg/mL caries DNA (211 bp) in 15 mL urine sample, suggesting that this method may be suitable for the extraction of genetic biomarkers for cfDNA-based liquid biopsy.
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Acknowledgments
We thank the Microtrac BEL Corp. for the zeta-potential measurement using Stabino.
Funding
This work was supported by grants (Kakenhi) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan and JSPS Core-to-Core Program, A. Advanced Research Networks.
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All clinical studies involving human urine samples were conducted in adherence to the procedure approved by the Human Ethics Committee of the School of Pharmacy in Showa University, and informed consent was received from the volunteers.
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Kato, M., Fujita, Y., Iizuka, T. et al. Extraction of urinary cell-free DNA by using triamine-modified silica particles for liquid biopsy. Anal Bioanal Chem 412, 5647–5652 (2020). https://doi.org/10.1007/s00216-020-02784-5
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DOI: https://doi.org/10.1007/s00216-020-02784-5