Monitoring mRNA in living cells in a 3D in vitro model using TAT-peptide linked molecular beacons

Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells

Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.

Polymeric siRNA gene delivery - transfection efficiency versus cytotoxicity

Within the field of gene therapy, there is a considerable need for the development of non-viral vectors that are able to compete with the efficiency obtained by viral vectors, while maintaining a good toxicity profile and not inducing an immune response within the body. While there have been many reports of possible polymeric delivery systems, few of these systems have been successful in the clinical setting due to toxicity, systemic instability or gene regulation inefficiency, predominantly due to poor endosomal escape and cytoplasmic release. The objective of this review is to provide an overview of previously published polymeric non-coding RNA and, to a lesser degree, oligo-DNA delivery systems with emphasis on their positive and negative attributes, in order to provide insight in the numerous hurdles that still limit the success of gene therapy.

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing

RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure–function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in RNA functions and regulations obtained from the studies of RNA structuromes. And finally, we propose potential directions for future improvements and studies.

Multi-targeting peptides for gene carriers with high transfection efficiency

Non-viral gene carriers for gene therapy have been developed for many years.

The interaction of QDs with RAW264.7 cells: nanoparticle quantification, uptake kinetics and immune responses study

Exposure to small QDs in high concentration in continuous cell culture results in cell death by apoptosis and necrosis co-existing within the same cell population.

Microprecision delivery of oligonucleotides in a 3D tissue model and its characterization using optical imaging

Despite significant potential of oligonucleotides (ONs) for therapeutic and diagnostic applications, rapid and widespread intracellular delivery of ONs in cells situated in tissues such as skin, head and neck cavity, and eye has not been achieved. This study was aimed at evaluating the synergistic combination of microneedle (MN) arrays and biochemical approaches for localized intratissue delivery of oligonucleotides in living cells in 3D tissue models. This synergistic combination was based on the ability of MNs to precisely deliver ONs into tissues to achieve widespread distribution, and the ability of biochemical agents (streptolysin O (SLO) and cholesterol conjugation to ONs) to enhance intracellular ON delivery. The results of this study demonstrate that ON probes were uniformly coated on microneedle arrays and were efficiently released from the microneedle surface upon insertion in tissue phantoms. Co-insertion of microneedles coated with ONs and SLO into 3D tissue models resulted in delivery of ONs into both the cytoplasm and nucleus of cells. Within a short incubation time (35 min), ONs were observed both laterally and along the depth of a 3D tissue up to a distance of 500 μm from the microneedle insertion point. Similar widespread intratissue distribution of ONs was achieved upon delivery of ON-cholesterol conjugates. Uniformity of ON delivery in tissues improved with longer incubation times (24 h) postinsertion. Using cholesterol-conjugated ONs, delivery of ON probes was limited to the cytoplasm of cells within a tissue. Finally, delivery of cholesterol-conjugated anti-GFP ON resulted in reduction of GFP expression in HeLa cells. In summary, the results of this study provide a novel approach for efficient intracellular delivery of ONs in tissues.

Biomaterial constructs for delivery of multiple therapeutic genes: a spatiotemporal evaluation of efficacy using molecular beacons

Gene therapy is emerging as a potential therapeutic approach for cardiovascular pathogenesis. An appropriate therapy may require multiple genes to enhance therapeutic outcome by modulating inflammatory response and angiogenesis in a controlled and time-dependent manner. Thus, the aim of this research was to assess the spatiotemporal efficacy of a dual-gene therapy model based on 3D collagen scaffolds loaded with the therapeutic genes interleukin 10 (IL-10), a potent anti-inflammatory cytokine, and endothelial nitric oxide synthase (eNOS), a promoter of angiogenesis. A collagen-based scaffold loaded with plasmid IL-10 polyplexes and plasmid eNOS polyplexes encapsulated into microspheres was used to transfect HUVECs and HMSCs cells.The therapeutic efficacy of the system was monitored at 2, 7 and 14 days for eNOS and IL-10 mRNA expression using RT-PCR and live cell imaging molecular beacon technology. The dual gene releasing collagen-based scaffold provided both sustained and delayed release of functional polyplexes in vitro over a 14 day period which was corroborated with variation in expression levels seen using RT-PCR and MB imaging. Maximum fold increases in IL-10 mRNA and eNOS mRNA expression levels occurred at day 7 in HMSCs and HUVECs. However, IL-10 mRNA expression levels seemed dependent on frequency of media changes and/or ease of transfection of the cell type. It was demonstrated that molecular beacons are able to monitor changes in mRNA levels at various time points, in the presence of a 3D scaffolding gene carrier system and the results complemented those of RT-PCR.

Intracellular nucleic acid interactions facilitated by quantum dots: conceptualizing theranostics

The concept of theranostics arises from the unification of both diagnostic and therapeutic applications into a single package. The implementation of nanoparticles, such as semiconductor quantum dots (QDs), to achieve theranostic applications, offers great potential for development of methods that are suitable for personalized medicine. Researchers have taken advantage of the physiochemical properties of QDs to elicit novel bioconjugation techniques that enable the attachment of multifunctional moieties on the surface of QDs. In this review, the diagnostic and therapeutic applications of QDs that feature the use of nucleic acids are highlighted with a particular emphasis on the possibility of combinatorial applications. Nucleic acid research is of particular interest for gene therapy, and is relevant to the understanding of gene regulation pathways and gene expression dynamics. Recent toxicity studies featuring multifunctional QDs are also examined. Future perspectives discussing the expected development of this field conclude the article.