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

TL;DR

Researchers developed a low-cost, fast method to isolate DNA and RNA from very few cells, including single cells, using magnetic nanoparticles, which could make genetic research more accessible and efficient.

Contribution

The study optimized a nucleic acid isolation method for single-cell applications, enabling high-throughput processing at lower costs.

Findings

The NAxtra method achieves comparable or better performance than existing kits in (RT)-qPCR detection.

It allows high-quality RNA extraction suitable for transcriptomics from limited cell quantities.

Automated processing handles 96 samples in 12–18 minutes, improving efficiency.

Abstract

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 min. 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. This advancement holds substantial promise for improving the accessibility and efficiency of NA research, particularly in studies involving scarce cellular materials.

The online version contains supplementary material available at 10.1038/s41598-025-05770-y.

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