Double-strand RNA binding

DSRM Double-stranded RNA binding motif E(MFP)B 2(2) 12(19) 1STU... 

Tian, B., Bevilacqua, PC., Diegelman-Parente, A., Mathews, M.B. The double-stranded-RNA-binding motif Interference and much more. Nat. Rev. Mol. Cell Biol. 2004, 5,1013-23. 

Nanduri S, Carpick BW, Yang Y, Williams BR, Qin J (1998) Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. Embo J 17 5458-5465... 

Khoo D, Perez C, Mohr I. Characterization of RNA determinants recognized by the arginine- and proline-rich region of Usll, a herpes simplex virus Type 1-encoded double-stranded RNA binding protein that prevents PKR activation. J Virol 2002 76(23) 11971-11981. 

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... 

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. 

This protocol uses propidium iodide (PI) as the fluorescent tracer for DNA content (3-6). PI binds to both double-stranded DNA and double-stranded RNA. Therefore, RNase will be used to reduce the double-stranded RNA resulting in only DNA staining. For alternative DNA-specific ligands and dyes, see Chapter 30. 

Fig. 1.56. Control of eIF-2 by phosphorylation. Phosphorylated eIF-2 GDP binds strongly to eIF-2B without nucleotide exchange occurring. Initiation of protein biosynthesis is not possible in this case.In reticulocytes, eIF-2 is subject to phosphorylation by the heme-regulated eIF-2-kinase (HRI). The activity of the dimeric HRI is regulated via the heme concentration. Another protein kinase that can phosphorylate and regulate eIF-2 is the RNA-dependent eIF2a-kinase (PKR). The latter is induced by interferons and activated by double stranded RNA.

The binding of interferons to their receptors induces a rapid increase in the transcription of particular genes and synthesis of corresponding proteins.196 202 One of the proteins induced is a double-stranded RNA-activated 2 -5 A synthase, which polymerizes ATP to a series of 2 -5 linked oligonucleotides containing triphosphates at the 5 termini.202-204 Double-stranded RNA is uncommon except in replicating viruses, and it is thought that the activation by dsRNA is related to establishment of an antiviral state. Another interferon-induced enzyme is the small subunit of eukaryotic protein synthesis initiation factor eIF-2. 

Silhavy, D., Molnar, A., Lucioli, A., Szittya, G., Hornyik, C., Tavazza, M. and Burgyan, J. (2002) A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO Journal 21, 3070-3080. 

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