Detection and Measurement of Chimeric RNAs by RT-PCR Using Novel RNA Extraction Method

Efficient nucleic acid extraction and purification are fundamental to cellular and molecular biology research but remain challenging for large-scale clinical RNA sequencing and PCR assays. This chapter introduces BLADE-R, a novel magnetic bead-based protocol that streamlines the RNA extraction process. BLADE-R integrates cell lysis and nucleic acid binding into a single step, followed by an innovative on-bead rinse to achieve nuclease-free separation of genomic DNA and RNA. The protocol's adaptability to a 96-well plate format enables simultaneous RNA purification from up to 96 human blood samples, significantly reducing time compared with single-sample methods. In this high-throughput setup, BLADE-R demonstrated no cross-contamination between wells during RNA purification, cDNA synthesis, and PCR. BLADE-R's versatility, efficiency, and suitability for low- and high-throughput applications make it an ideal method for RNA preparation in clinical and research settings, particularly for detecting and measuring chimeric RNAs using RT-PCR and sequencing assays. This protocol is especially advantageous in resource-limited environments, facilitating robust and scalable RNA extraction workflows.