Double short hairpin RNA

Masuda H, Watanabe N, Naruoka H et al (2010) Synthesis, gene-silencing activity and nuclease resistance of 3 -3 -lin]ced double short hairpin RNA. Bioorg Med Chem 18 8277-8283... 

Moreover, double immunoliposomes were developed in order to treat intracranial human brain cancer in mice [406], The mAbs used were the rat 8D3 mAb to the mouse transferrin receptor and the mAb against the HIR. RNAi (intereference RNA) is a new antisense gene therapy, where an expression plasmid encodes for a shRNA (short hairpin RNA). The shRNA is processed in the cell to an RNA duplex. The latter mediated RNAi. Indeed, weekly i.v. RNAi gene therapy reduced tumor expression of immunoreactive EGFR and caused an 88% increase in survival time of mice with advanced intracranial brain cancer. 

Single stranded RNAs consisting of 100s of bases fold back on themselves and undergo complementary baseparing to form double-stranded short-hairpin RNA (shRNA). The loop of the hair-pin is excised by endonucleases, e.g Dicer, to produce multiple functional miRNAs. 

Figure 13.14 Schematic representation of RNA Interference. Small interfering RNA (siRNA) is generated by Dicer (RNase) cleavage of a short hairpin RNA (shRNA) into small double-stranded RNA (dsRNA) of 21-25 nucleotide lengths, or transfected into the cell. The transfected siRNA is phosphorylated at 5 -ends by an endogenous kinase. The 5 -phosphorylated siRNA is incorporated into RNA-induced silencing complex (RISC) and unfolded. The antisense strand targets the RISC to homologous mRNA (sequence complementary to the siRNA guide) which is then cleaved by an endonuclease in the RISC complex (termed Sheer). The mRNA initially cleaved by Sheer is degraded by exonucleases and thus silenced...

FIGURE 15.2 The mechanism of RNA interference (RNAi). Exogenous double stranded RNA or endogenous hairpin RNA is cleaved by Dicer to make short interfering RNAs (siRNAs). These are incorporated into the RNA-induced silencing complex (RISC). Upon activation with ATP, the siRNA unwinds and the RISC complex mediates the cleavage of the target mRNA. 

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

The structures of RNA molecules consist of a single polymer chain of nucleotides with the same bases as DNA, with the exception of thymine, which is replaced by uracil, which forms a complementary base pair with adenine (Figure 1.33(a)). These chains often form single stranded hairpin loops separated by short sections of a distorted double helix formed by hydrogen bonded complementary base pairs (Figure 1.33(b)). 

The two species are quite similar the variations come from their source. MicroRNA comes from short endogenous hairpin loop structures, while siRNA molecules are produced from long double-stranded RNA molecules or giant hairpin molecules. The mature miRNA molecules are 22 nucleotide duplexes and usually repress translation of target mRNA sequences. The siRNAs are part of the antiviral defense system of the cell. 

RNA double helices are frequently interrupted by short sequences of nucleotides on both strands which cannot form standard Watson-Crick base pairs. These regions which connect two Watson-Crick helices are historically referred to as internal loops in analogy to hairpin loops which coimect the ends of helices. A symmetric internal loop has an equal number of nucleotides on opposing strands, while an asymmetric internal loop has a different number of nucleotides on the two strands. Figure 1 schematically defines internal loops. 

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