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Engineering Small Interfering RNAs by Strategic Chemical Modification

Synthetic small interfering RNAs (siRNAs) have revolutionized functional genomics in mammalian cell cultures due to their reliability, efficiency, and ease of use. This success, however, has not fully translated into siRNA applications in vivo and in siRNA therapeutics where initi ...

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Design and Screening of siRNAs Against Highly Structured RNA Targets

RNA silencing is an invaluable tool to interrogate gene function. The cytoplasmic delivery of small interfering RNAs (siRNAs) complementary to a gene of interest results in cleavage and degradation of the target mRNA. Given the potential to target virtually any RNA, siRNA-based therape ...

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Designing Functional siRNA with Reduced Off-Target Effects

RNA interference (RNAi) mediated by small interfering RNA (siRNA) is now widely used to knock down gene expression in a sequence-specific manner, making it a powerful tool not only for studying gene functions but also for therapeutic applications. siRNA decreases the expression level of the ...

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Methods for Selecting Effective siRNA Target Sequences Using a Variety of Statistical and Analytical Techniques

Short interfering RNA (siRNA) has been widely used for studying gene function in mammalian cells but varies markedly in its gene silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported recently, there are only a few cons ...

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Downregulation of Plant Genes with miRNA-Induced Gene Silencing

In plants, some microRNAs (miRNAs) can trigger the production of secondary small interfering RNAs (siRNAs) from their targets. miRNA-induced gene silencing (MIGS) exploits this unique feature to efficiently downregulate gene expression. The simple flanking of a sequence of inter ...

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What Parameters to Consider and Which Software Tools to Use for Target Selection and Molecular Design of Small Interfering RNAs

The design of small gene silencing RNAs with a high probability of being efficient still has some elements of an art, especially when the lowest concentration of small molecules needs to be utilized. The design of highly target-specific small interfering RNAs or short hairpin RNAs is even a great ...

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Designing Effective amiRNA and Multimeric amiRNA Against Plant Viruses

RNA-mediated virus resistance is increasingly becoming a method of choice for antiviral defense in plants when effective natural resistance is unavailable. In this chapter we discuss the design principles of artificial micro RNA (amiRNA), in which a natural miRNA precursor gene is modi ...

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Construction of shRNA Expression Plasmids for Silkworm Cell Lines Using Single-Stranded DNA and Bst DNA Polymerase

Transfection of short hairpin RNA (shRNA) expression plasmids is conventionally performed for gene-specific knockdown in cultured mammalian and insect cells. Here, I describe a simple method to synthesize an inverted repeat DNA in a U6 small nuclear RNA promoter-based parent vector u ...

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Design of RNAi Reagents for Invertebrate Model Organisms and Human Disease Vectors

RNAi has become a very versatile tool to silence gene expression in a variety of organisms, in particular when classical genetic methods are missing. However, the application of this method in functional studies has raised new challenges in order to design RNAi reagents that minimize false po ...

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Production and Application of Long dsRNA in Mammalian Cells

Double-stranded RNA (dsRNA) is involved in different biological processes. At least three different pathways can respond to dsRNA in mammals. One of these pathways is RNA interference (RNAi) where long dsRNA induces sequence-specific degradation of transcripts carrying sequenc ...

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Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers

Synthetic shRNAs that are too short to be Dicer substrates (short shRNAs or sshRNAs) can be highly potent RNAi effectors when properly designed, with activities similar to or more potent than the more commonly used siRNAs targeting the same sequences. sshRNAs can be designed in two possible ori ...

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Bifunctional Short Hairpin RNA (bi-shRNA): Design and Pathway to Clinical Application

The discovery of RNA interference (RNAi) engendered great excitement and raised expectations regarding its potential applications in biomedical research and clinical usage. Over the ensuing years, expanded understanding of RNAi and preliminary results from early clinical t ...

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Design of Lentivirally Expressed siRNAs

RNA interference (RNAi) has been widely used as a tool for gene knockdown in fundamental research and for the development of new RNA-based therapeutics. The RNAi pathway is typically induced by expression of ∼22 base pair (bp) small interfering RNAs (siRNAs), which can be transfected into cells. ...

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Short Hairpin RNA-Mediated Gene Silencing

Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNAs (shRNAs) for targeted gene silencing has become a benchmark technology. Using plasmid and viral vectoring systems, the transcription of shRNA precursors that are effectiv ...

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Designing Efficient and Specific Endoribonuclease-Prepared siRNAs

RNA interference (RNAi) has grown to be one of the main techniques for loss-of-function studies, leading to the elucidation of biological function of genes in various cellular systems and model organisms. While for many invertebrates such as Drosophila melanogaster (D. melanogaster) a ...

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Strategies for Designing and Validating Immunostimulatory siRNAs

Specific clinical applications of RNA interference (RNAi) can benefit from a concurrent activation of the immune system. This is the case for small interfering RNAs (siRNAs) with antitumor or antiviral activities. This chapter provides a brief overview of the strategies reported to date ...

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Delivery of Plasmid DNA to Mammalian Cells Using PolymerGold Nanorod Assemblies

Functionalized and surface-modified gold nanorods (GNRs) have emerged as promising vehicles for the delivery of several therapeutic agents. Ease of functionalization, increased stability, biocompatibility, and size-dependent plasmonic properties make gold nanorods ...

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A Method to Encapsulate Molecular Cargo Within DNA Icosahedra

DNA self-assembly has yielded various polyhedra based on platonic solids. DNA polyhedra can act as nanocapsules by entrapping various molecular entities from solution and could possibly find use in targeted delivery within living systems. A key requirement for encapsulation is that ...

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Permeabilization of Cell Membrane for Delivery of Nano-objects to Cellular Sub-domains

Delivery of nano-objects to specific cellular sub-domains is a challenging but intriguing task. There are two major barriers on the way of a nano-object to its intracellular target: (1) the cell membrane and (2) the intracellular barriers. The former is a common issue for all nanomedicine and a matt ...

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Methods for Isolation and Identification of Nanoparticle-Containing Subcellular Compartments

Nanoparticle-based drug delivery systems have considerable potential for improvement of drug stability, bioavailability, and reduced dosing frequency. Important technological advantages of nanoparticles include high carrier capacity across biological membran ...

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