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Rapid DNA and RNA isolation from few or single cells using low-cost NAxtra magnetic nanoparticles

ABSTRACT: A low-cost nucleic acid (NA) isolation method for purification of total NA, DNA or RNA from two- or three-dimensional cell culture was recently developed at the Norwegian University of Science and Technology (NTNU) based on NAxtra magnetic nanoparticles. The method displayed similar yields to alternative isolation kits, as well as significant improvement in cost and speed. In molecular research, NA isolation from rare or single cells is of increasing interest. Here, we improved the sensitivity of the NAxtra-based NA isolation method to allow mid- to high-throughput purification from 10 000 cells down to single cells. Automated processing on KingFisher (Thermo Scientific) robot systems can be performed in 12-18 minutes for 96 samples. This method is considerably cheaper and faster than similar purification alternatives, while achieving comparable or superior detection by (RT)-qPCR. In addition, high-quality transcriptomics data can be obtained from RNA extracted from few or single cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE284534 | GEO | 2025/07/09

REPOSITORIES: GEO

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Rapid DNA and RNA isolation from few or single cells using low-cost NAxtra magnetic nanoparticles

Project description:A novel, cost-effective nucleic acid (NA) isolation method for purifying total NA, DNA, or RNA from both two- and three-dimensional cell cultures has been developed at the Norwegian University of Science and Technology utilizing NAxtra magnetic nanoparticles. This method achieves comparable yields to existing isolation kits while offering significant improvements in cost and processing speed. However, the original protocol was not optimized for small-cell numbers or single-cell applications. Given the growing interest in single-cell and rare-cell population studies, there is a critical need for more sensitive isolation techniques. In this study, we have enhanced the sensitivity of the NAxtra-based isolation method to facilitate mid- to high-throughput purification from as few as 10,000 cells down to single cells. Automated processing using KingFisher systems enables the rapid handling of 96 samples within 12-18 minutes. Our findings indicate that this method not only matches but can exceed the performance of existing alternatives in (RT)-qPCR detection while being significantly more economical and efficient. Additionally, it enables the extraction of high-quality RNA suitable for transcriptomics analyses from limited cell quantities, including single cells, as indicated by comparison with the Evercode Whole Transcritome v2 kit. This advancement holds substantial promise for improving the accessibility and efficiency of nucleic acid research, particularly in studies involving scarce cellular materials.

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