Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases

Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.     

siRNA分子设计研究进展

为了设计高效的siRNA（Short-interfering Ribonucleic Acid）分子、最大限度地减少siRNA分子的脱靶效应（off-target effects）,siRNA分子设计已经成为热门研究领域。siRNA分子设计主要是基于序列和能量特征,以及靶标的二级结构特征,基于这些特征设计的siRNA分子已经有了较高的抑制基因表达的效率。RNAi（RNA in-terference）在基因发现以及疾病治疗领域已有非常广泛的应用,就siRNA分子设计近年的研究进展作一综述,为今后siRNA研究提供参考。     

New innovations in agricultural biotech: Consumer acceptance of topical RNAi in rice production

To test the market viability of a non-GMO topical RNAi insect control, we conducted a Willingness-To-Pay (WTP) survey in the USA, Canada, Australia, France, and Belgium to elicit whether consumers need a premium or discount for: (1) a hypothetical GMO rice variety using the Bacillus thuringiensis (Bt) gene for insect control; and (2) a hypothetical non-GMO rice variety using topical RNAi spray for insect control. The survey was designed based on a Multiple Price List (MPL) format where respondents selected their preferred insect control technology; i.e., conventional, GMO Bt, or non-GMO RNAi, at different prices. Participants' responses were analyzed using an interval regression model to generate WTP premiums and discounts for each country with control variables for demographic influences. Further, we asked consumers their Willingness-To-Consume (WTC) food produced with GM and RNAi technologies respectively and evaluated WTC differences using a McNemar matched pairs test in each country. The results from our study clearly show that: (1) consumers in the USA, Canada, Australia, and France still require a discount for rice produced with topical RNAi compared to conventionally-produced rice (p < 0.05), (2) consumers in the USA, Canada, Australia, France, and Belgium would need an additional 30–40% discount to purchase Bt rice over rice produced with topical RNAi (p < 0.05), and (3) consumers in all countries were more willing to consume rice produced with non-GM RNAi than with GM Bt technology (p < 0.05). These findings suggest consumers differentiate among biotechnology solutions and consumers may prefer topical RNAi insect control to transgenic GMO insecticides.     

Plastid Transformation of Micro-Tom Tomato with a Hemipteran Double-Stranded RNA Results in RNA Interference in Multiple Insect Species

Plant-mediated RNA interference (RNAi) holds great promise for insect pest control, as plants can be transformed to produce double-stranded RNA (dsRNA) to selectively down-regulate insect genes essential for survival. For optimum potency, dsRNA can be produced in plant plastids, enabling the accumulation of unprocessed dsRNAs. However, the relative effectiveness of this strategy in inducing an RNAi response in insects using different feeding mechanisms is understudied. To investigate this, we first tested an in vitro-synthesized 189 bp dsRNA matching a highly conserved region of the v-ATPaseA gene from cotton mealybug (Phenacoccus solenopsis) on three insect species from two different orders that use leaf-chewing, lacerate-and-flush, or sap-sucking mechanisms to feed, and showed that the dsRNA significantly down-regulated the target gene. We then developed transplastomic Micro-tom tomato plants to produce the dsRNA in plant plastids and showed that the dsRNA is produced in leaf, flower, green fruit, red fruit, and roots, with the highest dsRNA levels found in the leaf. The plastid-produced dsRNA induced a significant gene down-regulation in insects using leaf-chewing and lacerate-and-flush feeding mechanisms, while sap-sucking insects were unaffected. Our results suggest that plastid-produced dsRNA can be used to control leaf-chewing and lacerate-and-flush feeding insects, but may not be useful for sap-sucking insects.     

Applications of mass spectrometry to the study of siRNA

RNA interference (RNAi) has quickly become a well‐established laboratory tool for regulating gene expression and is currently being explored for its therapeutic potential. The design and use of double‐stranded RNA oligonucleotides as therapeutics to trigger the RNAi mechanism and a greater effort to understand the RNAi pathway itself is driving the development of analytical techniques that can characterize these oligonucleotides. Electrospray (ESI) and MALDI have been used routinely to analyze oligonucleotides and their ability to provide mass and sequence information has made them ideal for this application. Reviewed here is the work done to date on the use of ESI and MALDI for the study of RNAi oligonucleotides as well as the strategies and issues associated with siRNA analysis by mass spectrometry. While there is not a large body of literature on the specific application of mass spectrometry to RNAi, the work done in this area is a good demonstration of the range of experiments that can be conducted and the value that ESI and MALDI can provide to the RNAi field. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:979–998, 2011     

整合siRNA技术的结核核酸疫苗的AAV载体构建与浓缩纯化

引进腺病毒相关病毒载体系统(AAV载体系统),并通过PCR、酶切、连接等分子克隆手段将之前对于结核研究的成果转移至该系统中,完成同时具备小干扰RNA( si-Mcl-1)和结核融合抗原(AG85B-ESAT6)表达单位的二重表达载体的构建.转染AAV-293细胞,包装重组AAV病毒颗粒(rAAV)并收集病毒.分别设计另...     

ROS‐Responsive Polymeric siRNA Nanomedicine Stabilized by Triple Interactions for the Robust Glioblastoma Combinational RNAi Therapy

Small interfering RNA (siRNA) holds inherent advantages and great potential for treating refractory diseases. However, lack of suitable siRNA delivery systems that demonstrate excellent circulation stability and effective at‐site delivery ability is currently impeding siRNA therapeutic performance. Here, a polymeric siRNA nanomedicine (3I‐NM@siRNA) stabilized by triple interactions (electrostatic, hydrogen bond, and hydrophobic) is constructed. Incorporating extra hydrogen and hydrophobic interactions significantly improves the physiological stability compared to an siRNA nanomedicine analog that solely relies on the electrostatic interaction for stability. The developed 3I‐NM@siRNA nanomedicine demonstrates effective at‐site siRNA release resulting from tumoral reactive oxygen species (ROS)‐triggered sequential destabilization. Furthermore, the utility of 3I‐NM@siRNA for treating glioblastoma (GBM) by functionalizing 3I‐NM@siRNA nanomedicine with angiopep‐2 peptide is enhanced. The targeted Ang‐3I‐NM@siRNA exhibits superb blood–brain barrier penetration and potent tumor accumulation. Moreover, by cotargeting polo‐like kinase 1 and vascular endothelial growth factor receptor‐2, Ang‐3I‐NM@siRNA shows effective suppression of tumor growth and significantly improved survival time of nude mice bearing orthotopic GBM brain tumors. New siRNA nanomedicines featuring triple‐interaction stabilization together with inbuilt self‐destruct delivery ability provide a robust and potent platform for targeted GBM siRNA therapy, which may have utility for RNA interference therapy of other tumors or brain diseases.