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Topic: DsRNA

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	New England Biolabs
		The dsRNA Ladder is a set of 7 annealed double-stranded RNA molecules produced by in vitro transcription of 14 linear DNA templates.
		This ladder is suitable for use as a size standard in dsRNA and RNAi analysis on both non-denaturing polyacrylamide and agarose gels.
		We recommend loading 1.0-1.5 µg of dsRNA Ladder, a running voltage of 4-10 V/cm, adding ethidium bromide to gels and running buffer at a final concentration of 0.5 µg/ml to effectively stain the bands during electrophoresis.
	www.neb.com /nebecomm/products_intl/productN0363.asp (242 words)

	RNA -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-11-06)
		Double-stranded RNA (dsRNA) is used as the genetic material of some RNA viruses and is involved in some cellular processes, such as (Click link for more info and facts about RNA interference) RNA interference.
		Double-stranded RNA (or dsRNA) is RNA with two complementary strands, similar to the DNA found in all "higher" cells.
		dsRNA forms the genetic material of some ((virology) ultramicroscopic infectious agent that replicates itself only within cells of living hosts; many are pathogenic; a piece of nucleic acid (DNA or RNA) wrapped in a thin coat of protein) viruses.
	www.absoluteastronomy.com /encyclopedia/r/rn/rna2.htm (940 words)

	Molecular characterization of the genome of a partitivirus from the basidiomycete Rhizoctonia solani -- Strauss et al. ...
		encoded by ORF 2 of dsRNA 2 exhibited a moderate degree of phylogeny
		Hyakumachi, M., Sumino, A., Ueda, I. and Shikada, E. Relationship between the presence of dsRNA in Rhizoctonia solani and pathogenicity.
		Lakshman, D. K., Jian, J. and Tavantzis, S. A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway.
	vir.sgmjournals.org /cgi/content/full/81/2/549 (3361 words)

	BioMed Central \| Full text \| Disruption of vitellogenin gene function in adult honeybees by intra-abdominal injection ...
		Furthermore, an unambiguous fragment with an apparent size similar to the template dsRNA (504 bp) was visualized in all adult injected bees with a mutant phenotype (Figure 2c).
		If this dsRNA is processed into small interfering RNA (siRNA) or another mobile signal [26] that is exported to the hemolymph, this would make the fat body a source of mobile silencing agents that probably could be more easily taken up by other tissues.
		It should be noted that the dsRNA template found in adult workers might be slightly smaller than the dsRNA injected into the bees (Figure 3a), but whether this is of biological relevance is not clear.
	www.biomedcentral.com /1472-6750/3/1 (4154 words)

	Ambion TechNotes 9(5): RNAi: Size Does Matter
		Similar reduced activities (in comparison to that of full length dsRNAs) were obtained with shorter dsRNA specific for either the 5' or the 3' end of U2AF
		Interestingly, the high level of silencing induced by the longer dsRNAs could be reached with the shorter dsRNAs by increasing the concentration of the shorter dsRNAs 2-3 fold (Figure 1D).
		Because yields of dsRNA synthesized and purified with the MEGAscript RNAi Kit are reproducibly higher for shorter dsRNA (Figure 1C), two to five time more experiments can be performed per transcription reaction with 300 to 600 nt long dsRNA.
	www.ambion.com /techlib/tn/95/959.html (293 words)

	Ambion - Labeling Long dsRNA with the Silencer siRNA Labeling Kit
		We have successfully labeled 40 to 80 pmol of dsRNA*, 400 to 1200 nt in length, with this protocol.
		The amount of dsRNA per reaction may need to be optimized according to the size and concentration of the dsRNA.
		Fluorescent labeling is commonly used by scientists to localize macromolecules, but it was not known whether the incorporation of a fluorophore into dsRNA would affect its ability to induce gene silencing.
	www.ambion.com /techlib/misc/labeling_dsRNA.html (514 words)

	A Comprehensive View of Regulation of Gene Expression by Double-Stranded RNA-Mediated Cell Signaling.
		Virtually nothing is known about how dsRNA affects viral and cellular gene expression and functions in a virally infected cell, although the role of PKR, the dsRNA-activated protein kinase, in inhibiting protein synthesis has been studied in cells infected with a variety of viruses (2).
		That this induction is direct and not mediated by induced IFN was convincingly demonstrated in IFN unresponsive cells and in cells that are devoid of the IFN gene locus (5, 6).
		Those in Group A are induced by dsRNA, IFN, or several viruses; genes in Group B are induced by IFN and viral infection; those in Group C are induced by dsRNA and viruses; and the Group D genes are induced by dsRNA and IFN.
	www.euchromatin.org /Geiss01.htm (4255 words)

	KU: Molecular Biosciences
		Double-stranded RNA (dsRNA) was discovered to have the ability to interfere with gene function in a sequence-specific manner in the model genetic organism Caenorhabditis elegans.
		dsRNA with sequence homology to that of an endogenous gene or transgene can induce silencing of the corresponding gene or transgene--a process that has been termed RNAi (for dsRNA-mediated genetic interference).
		RNAi is an mRNA degradation mechanism that is triggered by dsRNA and is principally active in the cytoplasm of cells.
	molecularbiosciences.ku.edu /faculty/timmons.shtml (265 words)

	IFN-{alpha} Sensitizes Human Umbilical Vein Endothelial Cells to Apoptosis Induced by Double-Stranded RNA -- Kaiser et ...
		Fresh medium containing dsRNA was then added, and cells were photographed at the indicated times that were at 3-min intervals to demonstrate morphologic changes of apoptosis.
		The dsRNA was at 100 µg/ml in A, C, and D, and at the indicated concentration in B.
		-pretreated HUVECs respond to dsRNA with nuclear translocation of RelA and IRF-3 and are sensitive to dsRNA-induced cell death in the presence of proteasome inhibitors.
	www.jimmunol.org /cgi/content/full/172/3/1699 (7827 words)

	Ds RNA Interference with Gene Expression: RNAi
		However, the resulting effects on an animal are referred to as a phenocopy since it copies the phenotype of a loss-of-function mutation of that gene, but is not really inherited like a true gene deletion would be.
		The dsRNA should include at least about 300 bp of coding sequence homology, although specific requirements for size and amount of coding sequence that must be present are not well understood.
		This indicates that the introduced dsRNA species must be able to move across cell boundaries freely.
	avery.rutgers.edu /WSSP/StudentScholars/project/introduction/RNAi.html (409 words)

	Activation of NF-{kappa}B by Double-Stranded RNA (dsRNA) in the Absence of Protein Kinase R and RNase L Demonstrates ...
		dsRNA triggers the phosphorylation, polyubiquitinylation, and proteosome-mediated degradation of I
		the dsRNA response (lanes 3, 6, 9, and 12).
		At 4 h later, the cells were harvested, total RNA was prepared, and the steady-state levels of expression of multiple cytokines were assessed in a multiprobe RNase protection assay as described in Materials and Methods.
	mcb.asm.org /cgi/content/full/21/1/61 (6364 words)

	Double-Stranded RNA Mycovirus from Fusarium graminearum -- Chu et al. 68 (5): 2529 -- Applied and Environmental ...
		The presence or absence of the 7.5-kb dsRNA was
		A 7.5-kb dsRNA was present in all of the F.
		Conserved sequence motifs in the RNA-dependent RNA polymerases (RdRp) (A) and helicases (B) of positive-strand RNA viruses, related dsRNA viruses, and the 7.5-kb dsRNA of strain DK21.
	aem.asm.org /cgi/content/full/68/5/2529 (4344 words)

	Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA -- Abels et al. 88 (4): 2737 -- ...
		The slowly moving bands (near 4 kb on the reference ladder) correspond to the 4.2 kb dsRNA molecule without the labeled fragments and the 4.2 kb dsRNA molecule ligated to 0.4 kb biotin- and digoxigenin-labeled ends, respectively.
		The dsRNA molecule is tethered to a magnetic bead by a biotin-streptavidin linkage and to the bottom glass surface of a flow cell using an antidigoxigenin-digoxigenin linkage.
		Inset: the ratio of the persistence length of dsRNA to the persistence length of dsDNA is nearly constant as a function of l, indicating the robustness of the technique.
	www.biophysj.org /cgi/content/full/88/4/2737 (4748 words)

	IngentaConnect Satellite and Defective RNAs of Cryphonectria hypovirus 3-Grand H... (Site not responding. Last check: 2007-11-06)
		DsRNA 4 is 937 nucleotides, excluding the poly(A) The first AUG of the polyadenylated strand of dsRNA 4 occurs eight residues in from the 5
		DsRNA 3 accumulation in infected cultures varied, but it was less abundant than dsRNA 4.
		DsRNA 3 was found to represent a head-to-tail dimer of dsRNA 4 linked by a poly(A)/(U) stretch of 40–70 residues.
	www.ingentaconnect.com /content/ap/vy/2000/00000276/00000001/art00548 (447 words)

	Model System Genomics
		We require 2 mg/ml of dsRNA in 10-20 microliters of injection buffer.
		In experiments where 200 or 300 embryos are injected for the same construct, we treat that as two or three separate orders.
		You can find our dsRNA submission form here.
	www.biology.duke.edu /model-system/FlyShop/dsRNA.htm (151 words)

	siRNA - The ASCB Community Forum
		The use of antisense RNA to interfere with a gene's activity in C. elegans was first utilised by Su Guo and Ken Kemphues to study par-1 ; however, it was reported that control sense RNA also produced a par-1 mutant phenotype (Cell 81: 611-20, 1995).
		'98 that it is the presence of dsRNA, formed from the annealing of sense and antisense strands present in the in vitro RNA preps, that is responsible for producing the interfering activity.
		The current model favors a catalytic mechanism by which the dsRNA unwinds slightly, allowing the antisense strand to base pair with a short region of the target endogenous message and marking it for destruction.
	www.ascb.org /forums/upload/index.php?act=findpost&pid=160 (1886 words)

	RNAi (Site not responding. Last check: 2007-11-06)
		This observation suggested that the dsRNA must be either replicated and/or function catalytically; models that have been mutually supported by further studies.
		Genetic and biochemical studies involving plants and flies as well as worms have uncovered similar processes in which the dsRNA is cleaved into ~23 bp short interfering RNAs (siRNAs) by an enzyme called Dicer (Bernstein et al., 2001; Hamilton and Baulcombe, 1999, Science 286: 950), thus producing multiple “trigger” molecules from the original single dsRNA.
		Thus, these results suggest that a separate or additional uptake mechanism may be required to transport the initial dsRNA across epithelial boundaries into the cytoplasm, and that further transport to other cells/tissues represents a second transport mechanism.
	www.macalester.edu /~montgomery/RNAi.html (1267 words)

	Journal of Inflammation \| Full text \| CXCR2 is critical for dsRNA-induced lung injury: relevance to viral lung infection
		Viral infections of epithelial cells are characterized by the generation of the pro-inflammatory molecule double-stranded RNA (dsRNA) during intracellular replication of viruses.
		Previous studies have demonstrated that mice exposed to a live virus via intranasal inoculation generate a systemic acute-phase response with maximal pulmonary chemokine response at one week that includes both CC and CXC chemokines and is mouse strain-dependent (response in BALB/c greater than in C57BL/6 mice) [45,46].
		Finally, a recent study examined the effects of inhibiting the CC chemokine receptor, CCR1, during live-virus exposure in mice and showed that mortality during pneumovirus infection was decreased [49].
	www.journal-inflammation.com /content/2/1/4 (6404 words)

	BioMed Central \| Full text \| Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus ...
		This is not surprising because a previous analysis of the stability of dsRNA molecules after delivery into leaves supported that most of the input dsRNA was relatively stable and persisted in the leaf several days after inoculation, even after exuberant watering [19].
		It is thought that the presence of the transgene encoded dsRNA switches on the host's PTGS response prior to the invasion of the virus, which in turn leads to the RNA degradation of the invading virus [27,1].
		Therefore, we propose that the bacterially expressed dsRNA activates the PTGS machinery in cells where replication of the virus genome is simultaneously initiated.
	www.biomedcentral.com /1472-6750/3/3 (5503 words)

	Finnzymes - Products - Phi6 dsRNA
		The dsRNA fragments are 2948 bp (S segment), 4063 bp (M) and 6374 bp (L) in length.
		The dsRNA is isolated from the wild-type bacteriophage Phi6 propagated in P.
		Phi6 dsRNA in a total concentration of 500 ng/µl in 10 mM Tris-HCl (pH 8.0), 1 mM EDTA.
	www.finnzymes.fi /rna/phi6-dsRNA.html (127 words)

	A Small Modulatory dsRNA Specifies the Fate of Adult Neural Stem Cells.
		Interestingly, the expression of NRSE dsRNA was highly restricted in the subgranular region of dentate gyrus, in a region where adult neurogenesis is continuously occurring (van Praag et al., 2002; Kempermann, 2003) (Figure 7), supporting the in vitro data that NRSE dsRNAs function at an early stage in neuronal differentiation (Figures 1 and 2).
		In this study, a dsRNA with a restrictive silencer element was identified as a functional transcriptional activator.Genes important for neuronal properties contain the NRSE sequence, which is recognized by the protein NRSF/REST (Palm et al., 1998; Schoenherr et al., 1996).
		Therefore, dsRNAs might be sequestered in specific cellular compartments through interaction with their cognate protein partner(s) to mediate effects in a spatial-temporal and sequence-dependent manner of target mRNA, DNA, and proteins.
	www.euchromatin.net /Kuwabara01.htm (9133 words)

	Gene Therapy - Intracellular-diced dsRNA has enhanced efficacy for silencing HCV RNA and overcomes variation in the ... (Site not responding. Last check: 2007-11-06)
		In conclusion, intracellular-diced dsRNA efficiently induces RNAi, and, despite the high rate of mutation in HCV, it should be a feasible therapeutic strategy for silencing HCV RNA.
		The rhDicer-cleaved siRNAs and dsRNAs were separated by electrophoresis on a nondenaturing 12% polyacrylamide gel and detected by ultraviolet shadowing on a Fluor-coated thin-layer chromatography plate (Ambion).
		To evaluate the cytotoxic effects of dsRNAs, cell viability was measured by metabolic conversion of 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodium salt (WST-8) using a Cell Counting Kit-8 (Wako, Tokyo, Japan) according to the manufacturer's protocol.
	www.nature.com /gt/journal/v13/n11/full/3302734a.html (5003 words)

	dsRNA viruses - Reoviridae - Reoviridae study group - Cystoviridae - Birnaviridae - Totiviridae: Home Page
		Identification of some comparable proteins of the dsRNA viruses
		Link to a blank form for addition of data for a 'new' dsRNA virus to this web site.
		These pages were created in support of the dsRNA Virus Symposia.
	www.iah.bbsrc.ac.uk /dsRNA_virus_proteins (149 words)

	RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA -- Parker et al. ...
		RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA -- Parker et al.
		Previous studies note that cooperative ligands bind to nucleic acid lattices in clusters, and as the binding density increases, the average size of the bound clusters increases (Kowalczykowski et al.
		The 40-bp dsRNA preparations contained minimal amounts of contaminating ssRNA, except for that used with the C terminus protein, and in this case the observed complex is with ssRNA.
	www.rnajournal.org /cgi/content/full/12/5/807 (5636 words)

	dsRNA Genetic Elements: Concepts and Applications in Agriculture, Forestry, and Medicine
		Our understanding of the nature, origin, and biological roles of double-stranded RNA found in fungi, plants, and animals has advanced greatly during the last five years.
		Because these genetic elements are capable of replication, they can be used to manage fungal diseases of crops, vegetables, turfgrass, fruit, and forest trees using genetic means rather than by environmentally hazardous chemicals.
		It is a compilation of the latest advances on dsRNA systems from yeast, filamentous fungi, plants, and animals.
	www.ramex.com /title.asp?id=7290 (290 words)

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