Quantitative analysis of sequential nucleic acid elution from silica paramagnetic beads

Abstract

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.