Rapid, reversible RNA/DNA precipitation using rare earth ion coordination

Abstract

Efficient recovery and removal of nucleic acids remain major challenges in molecular biology, diagnostics, and viral-vector manufacturing. Conventional precipitation methods often require organic solvents, low temperatures, and extended centrifugation, while nuclease-based contaminant removal can be incomplete and/or is incompatible with downstream workflows. Here, we evaluate NADA, a trivalent rare earth-based reagent, for rapid, solvent-free precipitation of RNA and DNA, and ALGO-mediated recovery of the full range of properties of unmodified RNA. Using hepatitis B virus pre-genomic RNA, lambda bacteriophage DNA, and the HBV nucleocapsid as model systems, we show that NADA rapidly sequesters both ssRNA and dsDNA from solution, reducing Midori Green nucleic acid fluorescence and UV absorption to baseline levels. The NADA complex prevents HBV core protein binding to the HBV pgRNA, and therefore triggering of nucleocapsid formation, even when added simultaneously with core protein, suggesting that lanthanide ion coordination, out-competes the cognate Cp for viral RNA-binding interactions. Recovery with ALGO restores pgRNA integrity and functionality, enabling subsequent assembly of the expected T=4/T=3 nucleocapsids. In contrast, pre-assembled nucleocapsids resist NADA-ALGO treatment, demonstrating coat protein capsid-mediated protection of encapsidated pgRNA. Similar outcomes for lambda dsDNA establish NADA/ALGO as a rapid, reversible, and selective alternative platform for nucleic acid precipitation, with potential applications in viral particle purification, contaminant removal, and RNA handling workflows.