RNA, double-stranded

The other important feature of the primary stmcture of RNA is the presence of the 2 -hydroxyl group in ribose. Although this hydroxyl group is never involved in phosphodiester linkages, it does impose restrictions on the heHcal conformations accessible to double-stranded RNA. 

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

Interferons [alFN, piFN and ylFN]. Interferons are a family of glycosylated proteins and are cytokines which are produced a few hours after cells have been infected with a virus. Interferons protect cells from viral infections and have antiviral activities at very low concentrations ( 3 x 10 M, less than 50 molecules are apparently sufficient to protect a single cell). Double stranded RNA are very efficient inducers of IFNs. There are three main types of IFNs. The aIFNs are synthesised in lymphocytes and the piFNs are formed in infected fibroblasts. The a and P families are fairly similar consisting of ca 166 to 169 amino acids. Although ylFNs are also small glycosylated proteins (ca 146 amino acids), they are different because they are not synthesised after viral infections but are produced by lymphocytes when stimulated by mitogens (agents that induced cell division). 

The specific protein-DNA interactions described in this book are all with DNA in its regular B-form, or, in some cases with distorted B-DNA. In biological systems DNA appears not to adopt the A conformation, although double-stranded RNA does preferentially adopt this conformation in vivo. Whether or not Z-DNA occurs in nature is a matter of controversy. However, the formation of A-DNA and Z-DNA in vitro does illustrate the large structural changes that DNA can be forced to undergo. 

Dicer represents the key enzyme in the RNAi pathway. Dicer is also known as Helicase with RNAse motif, heRNA, Helicase-moi, K12H4.8-like, or KIAA0928. Dicer produces cleaves long double-stranded RNA into small pieces of about 21-23 nucleotides. These so-called siRNA duplexes produced by the action of Dicer contain 5 -phosphates and free 3 -hydroxylgroups... 

Double stranded (ds) RNA is not a constituent of a normal cells but is produced during replication of many RNA and DNA viruses either as an obligatory intermediate or as a side product. As a foreign molecule, double stranded RNA induce the secretion of interferon (EFN) from lymphocytes, neutrophils and fibroblasts. 

Small interfering RNAs (siRNA) are the mediators of gene-specific silencing by RNA interference. SiRNA stands for small interfering RNA duplexes. They are typically 21-23 bp in length. SiRNA were either chemically synthesised for experimental purposes or produced by Dicer-mediated cleavage of long double-stranded RNA. 

Dose-response Curves Double Stranded RNA Downregulation... 

HCV drugs with a direct antiviral mode of action are needed for the treatment of chronic HCV infection. The NS3 protease, NS3 heficase (which localizes to the carboxy-terminal domain of NS3 and catalyzes the unwinding of the double stranded RNA in a 3 to 5 direction (Tai et al. 1996)), and NS5B RNA polymerase... 

The antiviral state induced by different types of IFNs is mediated by various IFN-induced proteins. The best-known antiviral effectors produced as a result of IFN cascade induction are shown in Table 2. They include 2 -5 oligoadenylate synthetase (2 -5 OAS), double-stranded RNA activated protein kinase (PKR), and myxovirus (Mx) proteins. Additional effectors include RNA-specific adenosine deaminase 1 (ADARl), the 20-kDa ISG product (ISG20), ISG54 and ISG56, and IFN-stimulated micro RNAs (Pedersen et al. 2007). 

PKR Double-stranded RNA-activated protein kinase A serine threonine kinase that phos-phorylates eIF2a on serine residue 51 when activated... 

Recently, the related phenomenon of RNA interference (RNAi) has attracted much attention [5]. RNAi occurs when a short (generally 21 nucleotides in length) double-stranded RNA (dsRNA) catalyticaUy represses the translation of a fully complementary mRNA sequence. The process appears to proceed via a complex formed between the antisense RNA strand and a protein with RNase activity [6]. Upon binding to the target mRNA sequence, the ribonucleoprotein complex initiates cleavage of the mRNA transcript thus preventing translation of intact protein. After dissociation from the truncated mRNAs, the ribonucleoprotein complex is free to act on other intact mRNAs. Such small interfering RNAs (siRNAs) have... 

Lactide/glycoUde polymers have been investigated for delivery of several other macromolecules. Synthetic double-stranded RNA, poly-isosinic acid/polycytidylic acid, a potent inducer of interferon, was formulated in a 53 47 copolymer of DL-lactide-co-glycoUde. The microspheres were evaluated in mice challenged with Right Valley fever virus. More than 16 days protection was afforded versus only 3 days for controls (137). 

Besides these pathways, specific kinases like mixed lineage kinase and double-stranded RNA-activated protein kinase (PKR) have been implicated in gpl20-mediated neuronal death (Bodner et al. 2002 Alirezaei et al. 2007). 

Identification of proteins that bind to Z-DNA added one further step to the establishment of the presence of Z-DNA in vivo and its possible biological role. Herbert and Rich [22] demonstrated an in vitro assay system where one type of double-stranded RNA adenosine deaminase, called DRAD-binding Z-DNA. There are evidences that topoisomerase II from Drosophila, hiunan and calf thymus recognizes a number of DNA shapes, including Z-DNA [34,35]. Bloomfield and coworkers [36] have found that the condensation of plasmids is enhanced by Z-DNA conformation in d(CG)n repeats. The information related to B-Z transition [31], the effect of ligands on it [28,29] and X-ray crystal structure data [37,38] appear to suggest that the possible biological role of this polymorphic form of DNA will be soon established. 

A virus-specific RNA RNA polymerase is needed, since the cell RNA polymerase will generally not copy double-stranded RNA (and ribosomes are not able to translate double-stranded RNA either). A wide variety of modes of viral mRNA synthesis are outlined in Figure. By convention, the chemical sense of the mRNA is considered to be of the plus (+) configuration. The sense of the viral genome nucleic acid is then indicated by a plus if it is the same as the mRNA and a minus if it is of oppposite sense. If the virus has double-stranded DNA (ds DNA), then mRNA synthesis can proceed directly as in uninfected cells. However, if the virus has a singlestranded DNA (ss DNA), then it is first converted to ds DNA and the latter serves as the template for mRNA synthesis with the cell RNA polymerase. 

If the virus has double-stranded RNA (ds RNA), this RNA serves as a template in a manner analogous to DNA. There are three classes of viruses with ss RNA and they differ in the mechanism by which mRNA is synthesized. In the simplest case, the incoming viral RNA is the plus sense and hence serves directly as mRNA, and copies of this viral RNA are also copied to make further mRNA molecules. In another class, the viral RNA has a minus (-) sense. In such viruses a copy is made (plus sense) and this copy becomes the mRNA. In the case of the retroviruses (causal agents of certain kinds of cancers and AIDS), a new phenomenon called reverse transcription is seen, in which virion ss RNA is copied to a double-stranded DNA (through a ss DNA intermediate) and the ds DNA then serves as the template for mRNA synthesis (thus ss RNA ss DNA ds DNA). Retrovirus replication is of unusual interest and complexity. 

Srivastava, S. P., Kumar, K. U., and Kaufman, R. J. (1998). Phosphorylation of eukaryotic translation initiation factor 2 mediates apoptosis in response to activation of the double-stranded RNA-dependent protein kinase. J. Biol. Chem. 273, 2416—2423. 

Shir A, Ogris M, Wagner E, Levitzki A (2006) EGF receptor-targeted synthetic double-stranded RNA eliminates glioblastoma, breast cancer, and adenocarcinoma tumors in mice. PLoS Med 3 e6... 

Stem A stretch of double-stranded RNA Loop A loop of RNA Hairpin loop A very short loop... 

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