RNA hydrolysis at mineral-water interfaces



The adsorption of DNA at mineral-water interfaces is well-established to increase its persistence in soils and sediments; however, adsorbed RNA in similar environments degrades rapidly, in some cases outpacing solution-phase degradation occurring over hours to days. Herein, we elucidate a novel abiotic mechanism by which RNA, but not DNA, degrades upon adsorption to surfaces of iron (oxyhydr)oxides such as goethite (α-FeOOH) that are abundant in soils and sediments. Upon adsorption to goethite, both single-stranded and double-stranded RNA hydrolyzed on the timescale of hours under environmentally relevant physicochemical conditions. The reaction products were consistent with iron present in goethite acting as a Lewis acid to accelerate non-selective hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to well-established acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. We further confirmed that contact of the RNA with the mineral surface is necessary for hydrolysis to occur by demonstrating RNA degradation was inhibited by compact RNA conformation at elevated ionic strength and competitive adsorption with orthophosphate and organic matter. In addition to goethite, we observed RNA hydrolysis was also catalyzed by hematite (α-Fe2O3), but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.


Supplementary material

Supplementary information
Sources of chemicals and molecular biological kits; sequence information; mineral synthesis and characterization; incubation conditions; extraction method development and validation; supplementary results.