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

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. Single-cell RNA sequencing of HAP1 cells using the Evercode Whole Transcriptome v2 kit (Parse Biosciences), for comparison with the RNA-seq data generated for cells from the same population using the novel NAxtra-based method (GEO accession number: GSE284534).