RNA Hydrolysis at Mineral–Water Interfaces

Abstract

As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to 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. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe 2 O 3 ) 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.

Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation

“…The increased persistence of RNA in the presence of DOM has broad environmental implications, specifically in the context of emerging applications of RNA. For example, the suppression of mineral-catalyzed hydrolysis of RNA by DOM could increase the persistence of dsRNA biopesticides in relevant soils and sediments . The increased persistence of dsRNA biopesticides may increase risks posed to nontarget organisms, particularly if bioactivity of dsRNA is retained upon binding by DOM.…”

“…An exception was made for the DOM stocks, which were filter-sterilized but not autoclaved to avoid modifications to the DOM chemical properties. In the binding experiments, lower molecular weight products were not detected via gel electrophoresis, ruling out unintended degradation. , Additionally, because DOM had an inhibitory effect on RNase I-mediated RNA degradation, as determined in the degradation experiments detailed below, the contribution of residual RNases in DOM solutions to RNA degradation was inferred to be negligible relative to RNase I added as a reagent.…”

“…The persistence of these dsRNA pesticides in environmental systems influences both their efficacy (particularly when applied exogenously , ) as well as their potential risk to nontarget organisms arising from unintended exposure. , Due to its centrality across these applications, the persistence of RNA in environmental systems must be better constrained by improved understanding of key fate processes. While some of these processes likely parallel processes that impact DNA fate (e.g., adsorption to surfaces), others (e.g., abiotic degradation or biodegradation) may diverge. ,, …”

Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries

“…12–15 However, a recent study suggests that adsorbed dsRNA molecules may also be destabilized due to mineral-catalyzed dsRNA hydrolysis over the timescale of days. 16…”

“…Adsorption of dsRNA molecules to mineral soil particle surfaces has been assessed only in a few previous studies. 16–19 By comparison, DNA adsorption to soil particles and soil organic matter has been extensively studied and is well understood. 12,13,15,20–47 This raises the question if the extensive information on DNA adsorption in soils is transferrable to dsRNA adsorption.…”