Quantitative analysis of sequential nucleic acid elution from silica paramagnetic beads

Paramagnetic bead-based capture and release is widely used for nucleic acid preparation in benchtop and automated workflows. In emerging magnetofluidic and cartridge-style point-of-care systems, sequential bead elution has only recently begun to be explored as a strategy to distribute limited nucleic acids across multiple reactions. In such designs, elution behavior becomes directly relevant to assay performance and multiplexing capacity. Here, we systematically examine multi-sequential elutions from silica paramagnetic beads and quantify each eluate by qPCR. We describe the data with a phenomenological, concentration-dependent, exponential-decay model and show that elution profiles depend on nucleic acid target size (soybean genomic DNA versus a short synthetic double-stranded DNA fragment, gBlock), starting concentration, and multiplexed (duplex) bead binding. We demonstrate reproducible nucleic acid signal across eight elutions, extract size-dependent decay constants, and evaluate model performance over a range of input concentrations. Duplex and alternating-trait experiments further show that the same framework can describe multi-target elution with limited data points per target. Together, these results provide a quantitative description of sequential nucleic acid elution from silica beads and a simple modeling approach that can inform the design of multi-step bead-based workflows.