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RNAi is fast emerging as a wonderful tool for inhibiting gene expression in a sequence specific manner. The applications of this technology are two-fold: to study gene function, and use as a therapeutic agent in treating many diseases. As a therapeutic agent it finds applications in antiviral treatments because RNAi has been shown to successfully inhibit virus replication. In a report published on 8 November, 2007, in the Retrovirology, Naito et al., describe the design of antiviral siRNA targeted against HIV-I. To create effective antiviral siRNAs against HIV is a daunting task as the virus mutates at a very high frequency. The researchers first analyzed the HIV-I group M sequences available in the Los Alamos HIV Sequence Database and then found those regions which are highly conserved. Using these conserved regions as target sites, they designed optimal antiviral siRNAs. 21-mer siRNA sequences were generated for all the possible HIV-I sequences. The conserved sequences identified in HIV-I genome included the TATA sequence, polyadenylation signal (AAUAAA), regions essential for viral replication regulation, the primer activation signal (PAS), primer binding site (PBS), packaging signal (ψ), central polypurine tract (cPPT), central termination sequence (CTS), and 3 polypurine tract (3 PPT). A total of 216 highly conserved (>70%) siRNA targets were identified. 41 siRNAs (23 siRNAs out of 216 mentioned above and 18 more siRNAs targeted against moderately conserved regions) were subjected to target mRNA cleavage assay for functional validation using real-time RT-PCR. HeLa cells were cotransfected with vector expressing reporter mRNA that contains the siRNA target site and the corresponding siRNA. Then the potency of siRNAs was monitored by real-time RT-PCR. siRNAs were evaluated for their antiviral efficacy against HIV subtypes B, B’, C and CRF01_AE.
The study clearly demonstrated that 39 out of the 41 siRNAs gave more than >60% silencing; and 26 of the 41 siRNAs effectively inhibited viral replication of all four strains by >80%. The results of the study are quite remarkable and point towards the efficient use of siRNA for inhibiting viral gene expression and replication. The study also paved the way for using siRNAs against divergent HIV-I strains. However, the extreme genetic diversity and high mutation rate of the virus has hindered the creation of a single siRNA effective against all HIV-I strains found in the world. The use of this technology for as a highly effective treatment might be possible in the future and this study could be applied to other pathogens like SARS, influenza virus, etc.

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