Engineered RNA Nanodesigns for Applications in RNA Nanotechnology

Afonin, Kirill A.; Lindsay, Brian; Shapiro, Bruce A.

doi:10.2478/rnan-2013-0001

Cited by 34 publications

(32 citation statements)

References 148 publications

(205 reference statements)

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“…Unlike multi-stranded DNA tiles, most existing for self-assembly RNA tiles fold from single stranded molecules (tecto-RNAs), and inter-tile bonds form via conserved tertiary motifs such as for example, loop-receptor 20, 21 or kissing loops 6,22,5 interactions. This approach has two main advantages: 1) binding patterns are pre-determined from libraries of known tertiary motifs with controllable geometry, and 2) correctly designed short single strands are less prone to local kinetic traps with respect to multiple, longer strands.…”

Section: Introductionmentioning

confidence: 99%

Programmable RNA microstructures for coordinated delivery of siRNAs

et al. 2016

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RNA is a natural multifunctional polymer, and is an essential component in both complex pathways and structures within the cellular environment. For this reason, artificial self-assembling RNA nanostructures are emerging as a powerful tool with broad applications in drug delivery and metabolic pathway regulation. To date, coordinated delivery of functional molecules via programmable RNA assemblies has been primarily done using nanosize RNA scaffolds. However, larger scaffolds could expand existing capabilities for spatial arrangement of ligands, and enable the controlled delivery of highly concentrated molecular loads. Here, we investigate whether micron-size RNA scaffolds can be assembled and further functionalized with different cargos (e.g. various siRNAs and fluorescent tags) for their synchronized delivery to diseased cells. Since known design approaches to build large RNA scaffolds are still underdeveloped, we apply, for the first time, a tiling method widely used in DNA nanotechnology. DNA tiles have been extensively used to build a variety of scalable and modular structures that are easily decorated with other ligands. Here, we adapt a double crossover (DX) DNA tile motif to design de novo DX RNA tiles that assemble and form lattices via programmed sticky end interactions. Because the assembly protocols used in DNA nanotechnology are not suitable for RNA assembly, we optimize them to guarantee high yield of RNA lattices. The resulting constructs are robust and modular with respect to the presence of distinct siRNAs and fluorophores. RNA tiles and lattices are successfully transfected in either human breast cancer or prostate cancer cells, where they efficiently knockdown the expression of target genes. Blood serum stability assays indicate that RNA lattices are more resilient to nuclease degradation when compared to individual tiles, thus making them better suited for therapeutic purposes. Overall, because of its design simplicity, we anticipate that this approach will be utilized for a wide range of applications in therapeutic RNA nanotechnology.

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Section: Introductionmentioning

confidence: 99%

Programmable RNA microstructures for coordinated delivery of siRNAs

et al. 2016

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“…Techniques for constructing nanoparticles that can both diagnose and target diseased cells have given RNA a new role in nanomedicine. Such functionalized nanostructures are able to down-regulate specific gene expression in cancerous cells, with positive results being confirmed by animal studies [5, 6, 8, 13, 14]. All this suggests that RNA molecules may offer a high degree of natural versatility and biologically relevant functionality when used as building blocks in the construction of nanomaterials [3, 5, 6, 15–20].…”

Section: Introductionmentioning

confidence: 95%

Computational and experimental characterization of RNA cubic nanoscaffolds

Afonin

Kasprzak

Bindewald

et al. 2014

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The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the dynamic behavior of non-compact, multi-stranded RNA-based nanocubes that can be used as nano-scale scaffolds carrying different functionalities. Modeling the nanocubes with our tool NanoTiler and exploring the dynamic characteristics of the models with ANM suggested relatively minor but important structural modifications that enhanced the assembly properties and thermodynamic stabilities. In silico and in vitro, we compared nanocubes having different numbers of base pairs per side, showing with both methods that the 10 bp-long helix design leads to more efficient assembly, as predicted computationally. We also explored the impact of different numbers of single-stranded nucleotide stretches at each of the cube corners and showed that cube flexibility simulations help explain the differences in the experimental assembly yields, as well as the measured nanomolecule sizes and melting temperatures. This original work paves the way for detailed computational analysis of the dynamic behavior of artificially designed multi-stranded RNA nanoparticles.

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“…The dicable RNAs are also called Dicer Substrate (DS) RNAs and are an important class of RNAi activators as they promote RISC loading [30,31]. DS RNAs are also used for intracellular Dicer-assisted release of siRNAs from various artificially designed nanoconstructs (Figure 1.4) [32][33][34].…”

Section: Rnai Activatorsmentioning

confidence: 99%

Triggering RNAi with multifunctional RNA nanoparticles and their delivery

Dao¹,

Viard²,

Martins³

et al. 2015

DNA and RNA Nanotechnology

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in the bloodstream, poor cellular uptake, and inefficient intracellular release. In an attempt to solve these issues, different types of RNAi therapeutic delivery strategies including multifunctional RNA nanoparticles are being developed. In this mini-review, we will briefly describe some of the current approaches.Keywords: RNA nanotechnology, RNA nanoparticles, RNA/DNA hybrids, RNA interference, siRNA, delivery IntroductionAccording to the Social Security Administration, average Americans that reach age 65 today most likely will live to be 84 years old [1]. However, with older age, the chances of contracting deadly diseases, such as cancer, increases dramatically. Some cancers (e.g. breast cancer) can be removed surgically but this does not guarantee that the disease will not return within a patient's lifetime. For other types of cancer (e.g. chronic lymphocytic leukemia), surgery may have very little effect (http://www. cancer.org). Other available treatments are chemo-and immunotherapies. However, these alternatives lack target specificity and cause severe toxic side effects affecting the growth of hair, nails, loss of appetite and blood cell count, just to name a few (http://www.cancer.org). Therefore, the advancements in biomedical technologies that provide safe and effective cancer treatment are in demand. Among the novel approaches is the recognition and use of specific intracellular RNA signatures (e.g. an overexpression of certain genes) that are especially important in detection and personalized treatments of cancers as well as viral infections, and autoimmune diseases [2][3][4]. The wide use of novel therapeutics based on target specific RNA-mediated gene silencing, called RNA interference or RNAi, will likely become the next breakthrough in cancer therapy. The first successful therapeutic knockdown of the endogenous gene, apolipoprotein B (ApoB), occurred in a 2004 study [5], only a few years after the original discovery of RNAi [6]. In 2010, DOI 10.1515/rnan-2015-0001 Received April 6, 2015 accepted May 6, 2015 Abstract: Proteins are considered to be the key players in structure, function, and metabolic regulation of our bodies. The mechanisms used in conventional therapies often rely on inhibition of proteins with small molecules, but another promising method to treat disease is by targeting the corresponding mRNAs. In 1998, Craig Mellow and Andrew Fire discovered dsRNA-mediated gene silencing via RNA interference or RNAi. This discovery introduced almost unlimited possibilities for new gene silencing methods, thus opening new doors to clinical medicine. RNAi is a biological process that inhibits gene expression by targeting the mRNA. RNAi-based therapeutics have several potential advantages (i) a priori ability to target any gene, (ii) relatively simple design process, (iii) sitespecificity, (iv) potency, and (v) a potentially safe and selective knockdown of the targeted cells. However, the problem lies within the formulation and delivery of RNAi therapeutics including rapid excretion, instab...

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Engineered RNA Nanodesigns for Applications in RNA Nanotechnology

Cited by 34 publications

References 148 publications

Programmable RNA microstructures for coordinated delivery of siRNAs

Programmable RNA microstructures for coordinated delivery of siRNAs

Computational and experimental characterization of RNA cubic nanoscaffolds

Triggering RNAi with multifunctional RNA nanoparticles and their delivery

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