Comparison of Nanomaterials for Delivery of Double-Stranded RNA in Caenorhabditis elegans

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

The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.

Gold nanoparticle design for RNA compaction

RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery.

Zein and lignin-based nanoparticles as soybean seed treatment: translocation and impact on seed and plant health

Zein nanoparticles (ZNPs) were synthesized with a cationic surfactant, didodecyldimethylammonium bromide (122.9 ± 0.8 nm, + 59.7 ± 4.4 mV) and a non-ionic surfactant, Tween 80 (118.7 ± 1.7 nm, + 26.4 ± 1.1 mV). Lignin-graft-poly(lactic-co-glycolic) acid nanoparticles (LNPs) were made without surfactants (52.9 ± 0.2 nm, − 54.9 ± 0.5 mV). Both samples were applied as antifungal seed treatments on soybeans, and their impact on germination and plant health was assessed. Treated seeds showed high germination rates (> 90% for all treatment groups), similar to the control group (100%). Root and stem lengths and the dry biomass of treated seeds were not statistically distinguishable from the control. Foliage from seed-treated plants was fed to larvae of Chrysodeixis includens with no differences in mortality between treatments. No translocation of fluorescently tagged particles was observed with fluorescence microscopy following seed treatment and germination. Nano-delivered azoxystrobin provided ~ 100% protection when LNPs were used. Results suggest ZNPs and LNPs are safe and effective delivery systems of active compounds for seed treatments.

RNA Interference-Based Forest Protection Products (FPPs) Against Wood-Boring Coleopterans: Hope or Hype?

Forest insects are emerging in large extension in response to ongoing climatic changes, penetrating geographic barriers, utilizing novel hosts, and influencing many hectares of conifer forests worldwide. Current management strategies have been unable to keep pace with forest insect population outbreaks, and therefore novel and aggressive management strategies are urgently required to manage forest insects. RNA interference (RNAi), a Noble Prize-winning discovery, is an emerging approach that can be used for forest protection. The RNAi pathway is triggered by dsRNA molecules, which, in turn, silences genes and disrupts protein function, ultimately causing the death of the targeted insect. RNAi is very effective against pest insects; however, its proficiency varies significantly among insect species, tissues, and genes. The coleopteran forest insects are susceptible to RNAi and can be the initial target, but we lack practical means of delivery, particularly in systems with long-lived, endophagous insects such as the Emerald ash borer, Asian longhorn beetles, and bark beetles. The widespread use of RNAi in forest pest management has major challenges, including its efficiency, target gene selection, dsRNA design, lack of reliable dsRNA delivery methods, non-target and off-target effects, and potential resistance development in wood-boring pest populations. This review focuses on recent innovations in RNAi delivery that can be deployed against forest pests, such as cationic liposome-assisted (lipids), nanoparticle-enabled (polymers or peptides), symbiont-mediated (fungi, bacteria, and viruses), and plant-mediated deliveries (trunk injection, root absorption). Our findings guide future risk analysis of dsRNA-based forest protection products (FPPs) and risk assessment frameworks incorporating sequence complementarity-based analysis for off-target predictions. This review also points out barriers to further developing RNAi for forest pest management and suggests future directions of research that will build the future use of RNAi against wood-boring coleopterans.

Delivery of short hairpin RNA in the neotropical brown stink bug, Euschistus heros, using a composite nanomaterial

The response of insects to orally delivered double-stranded RNA ranges widely among taxa studied to date. Long dsRNA does elicit a response in stink bugs but the dose required to achieve an effect is relatively high compared to other insects such Colorado potato beetle or western corn rootworm. Improving the delivery of dsRNA to stink bugs will improve the likelihood of using RNA-based biocontrols for the management of these economically important pests. Short hairpin RNA (shRNA) is a useful molecule with which to test improvements in the delivery of double stranded RNA in the neotropical brown stink bug, Euschistus heros, since shRNA alone does not elicit a clear effect like that for long dsRNA. Here, we show for the first time the oral delivery of shRNA triggering RNA interference (RNAi) in E. heros using 4 nm cerium oxide nanoparticles (CeO₂ NPs) coated with diethylamioethyl dextran (Dextran-DEAE) as a carrier. We identified particle properties (coating composition and degree of substitution, hydrodynamic diameter, and zeta potential) and shRNA loading rates (Ce:shRNA mass ratio) that resulted in successful transcript reduction or RNAi. When the Z-average diameter of CeO₂ Dextran-DEAE-shRNA NP complex was less than 250 nm and the zeta potential was in the 15-25 mV range (Ce:shRNA mass ratio of 0.7:1), significant mortality attributed to RNAi was observed with a shRNA concentration in feeding solution of 250 ng/μl. The degradation of the targeted troponin transcript by NP-delivered shRNA was equivalent to that observed with long dsRNA, while naked shRNA transcript reduction was not statistically significant. Elemental mapping by synchrotron X-ray fluorescence microprobe confirmed uptake and distribution of Ce throughout the body with the highest concentrations found in gut tissue. Taken together, our results suggest that a nanoparticle delivery system can improve the delivery of RNA-based biocontrols to E. heros, and therefore its attractiveness as an application in the management of this important pest in soybean production.

dsRNA Uptake in Plant Pests and Pathogens: Insights into RNAi-Based Insect and Fungal Control Technology

Efforts to develop more environmentally friendly alternatives to traditional broad-spectrum pesticides in agriculture have recently turned to RNA interference (RNAi) technology. With the built-in, sequence-specific knockdown of gene targets following delivery of double-stranded RNA (dsRNA), RNAi offers the promise of controlling pests and pathogens without adversely affecting non-target species. Significant advances in the efficacy of this technology have been observed in a wide range of species, including many insect pests and fungal pathogens. Two different dsRNA application methods are being developed. First, host induced gene silencing (HIGS) harnesses dsRNA production through the thoughtful and precise engineering of transgenic plants and second, spray induced gene silencing (SIGS) that uses surface applications of a topically applied dsRNA molecule. Regardless of the dsRNA delivery method, one aspect that is critical to the success of RNAi is the ability of the target organism to internalize the dsRNA and take advantage of the host RNAi cellular machinery. The efficiency of dsRNA uptake mechanisms varies across species, and in some uptake is negligible, rendering them effectively resistant to this new generation of control technologies. If RNAi-based methods of control are to be used widely, it is critically important to understand the mechanisms underpinning dsRNA uptake. Understanding dsRNA uptake mechanisms will also provide insight into the design and formulation of dsRNAs for improved delivery and provide clues into the development of potential host resistance to these technologies.