96 shRNAs designed for maximal coverage of HIV-1 variants

Mcintyre, Glen J; Groneman, Jennifer Lynne; Yu, Yi-Hsin; Jaramillo, Angel B.; Shen, Sylvie; Applegate, Tanya

doi:10.1186/1742-4690-6-55

Cited by 41 publications

(48 citation statements)

References 49 publications

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“…5c). The loop sequence followed a previously described format of 8 nt, where the nucleotide N is complementary to the target site (45). Contrasting results for siRNAs (Fig.…”

Section: Resultsmentioning

confidence: 95%

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Scarborough

Adams

Daher³

et al. 2015

Antimicrob Agents Chemother

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We have previously identified a target site in HIV-1 RNA that was particularly accessible to a ribozyme and a short hairpin RNA (shRNA). To design small interfering RNAs (siRNAs) targeting this site, we evaluated the effects of siRNAs with different lengths on HIV-1 production. The potency and efficacy of these siRNAs were dependent on the length of their intended sense strand with trends for symmetrical and asymmetrical formats that were similar. Although a typical canonical format with a 21-nucleotide (nt) sense strand was effective at inhibiting HIV-1 production, Dicer substrate siRNAs (dsiRNAs) with the longest lengths (27 to 29 nucleotides) were the most effective. Induction of double-stranded RNA immune responses and effects on cell viability were not detected in cells transfected with different siRNAs, suggesting that the differences observed were not related to indirect effects on HIV-1 production. For the corresponding shRNA designs, a different trend in potency and efficacy against HIV-1 production was observed, with the most effective shRNAs having stem lengths from 20 to 27 bp. Our results highlight the importance of evaluating different designs to identify the best siRNA and shRNA formats for any particular target site and provide a set of highly effective molecules for further development as drug and gene therapies for HIV-1 infection.

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“…5c). The loop sequence followed a previously described format of 8 nt, where the nucleotide N is complementary to the target site (45). Contrasting results for siRNAs (Fig.…”

Section: Resultsmentioning

confidence: 95%

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Scarborough

Adams

Daher³

et al. 2015

Antimicrob Agents Chemother

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“…Meanwhile, molecular research of HIV infection in MSM is also needed. RNAi technology is a powerful tool to silence target gene expression in vitro and in vivo [27,11], and has been successfully used as an effective approach to inhibit the HIV replication [17,29,35]. The use of RNAi to inhibit HIV-1 represents a novel and potentially powerful antiviral strategy.…”

Section: Discussionmentioning

confidence: 99%

“…Actually, RNAi has been exploited in gene therapy strategies for HIV-1 [9,24,33]. It has been reported that about 200 published siRNAs and shRNAs are tested against HIV-1 [17], most of HIV genes and regular sequences are successfully targeted for RNAi [1,10,16].…”

Section: Introductionmentioning

confidence: 99%

Silencing of HIV-1 gag gene from epidemic strains among men who have sex with men (MSM) in Tianjin, China by a broad-spectrum short hairpin RNA

Liang

Wang

et al. 2014

VirusDis.

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RNA interference (RNAi) has been successfully used as a promising method to inhibit the replication of different viruses, including human immunodeficiency virus (HIV). Gene mutation is a hurdle for the anti-HIV by RNAi. Although prone to mutation, some genes are conserved and limited in functionally important regions. The gag gene is conserved in different subtypes and plays an important role in the assembly of HIV viral particle. Here, we identified subtypes and conserved sequences within forty-four gag genes from the epidemic strains among men who have sex with men. Three subtypes of gag gene, including CRF01_AE (47.7 %), CRF07_BC (40.9 %) and B (11.4 %) were analyzed by online blast. We designed five small hairpin RNAs (shRNAs) based on the conserved sequences. The gag-EGFP fusion transcript reporter system was used to select the most efficient shRNA. Among the five candidate shRNAs, gag-shRNA-3 represented a broad-spectrum inhibition against all chosen targets. This broad-spectrum shRNA diminished the titer of subtypes B and C of HIV-1 for a hundred orders of magnitude. The gag-shRNA-3 described here is a potential therapeutic agent in the HIV-1 gene therapy.

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“…Wt-(Wild type) Virions, Viruses, Proviruses, transcript et cetera will be used to indicate respectively infective HIV Virions, Viruses, Proviruses, transcript et cetera that can be found in the population. The shRNA sequences transducted by H-Vectors and related siRNAs are to be designed to target specific wt-HIV genes and transcripts, such as Gag, Pol, Env or Tat, Rev and Nef genes and their transcripts; a very good review about possible shRNAs with these characteristics can be found in Mcintyre et al [15]. Specifically, it seems that the early transcribed Tat, Rev and Nef genes [16] could be good candidates to be used to interfere with HIV infection [17].…”

Section: The Hypothesismentioning

confidence: 99%

A novel antiviral approach

Arancio¹

2012

Medical Hypotheses

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a b s t r a c t Viral infections are often the etiological agents of severe acute and chronic human diseases. Their peculiar biology usually leads to the need of design specific therapies for each virus, and the eradication of the viruses and the healing of the patients very often are not reached also after decades of theoretical and applied researches. HIV is a classical example of how the efforts of the researchers may be disappointed in eradicating a virus infection in an infected patient. Here I present a hypothesis for a new antiviral approach that may be suitable for the treatment of HIV infected patients. The same approach, with opportune modifications, may be also applied as healing strategy for a wide set of viruses infections. In brief, my idea is to use the retrotranscription machinery and the packaging system of HIV infected cells to amplify the interfering effects of siRNAs directed against HIV genes and transcripts. The coding sequences for the interfering RNAs are brought to the infected cells via modified HIV virions deficient for structural viral genes that will use the resident viral activities of HIV infected cell as helpers. The use of this strategy will probably lead to an intracellular, intercellular and systemic amplification of the specific virus-targeted interfering activities. Moreover this strategy may show novel levels of interference: a competition between the deficient and wild type viruses for the packaging molecules and the possibility of homologous recombination between the deficient and wild type viruses that may lead in turn to the formation of recombinant non infectious viruses, and the removing of wild type provirus sequence from the host genome of infected cells by recombination.

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96 shRNAs designed for maximal coverage of HIV-1 variants

Cited by 41 publications

References 49 publications

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Effective Inhibition of HIV-1 Production by Short Hairpin RNAs and Small Interfering RNAs Targeting a Highly Conserved Site in HIV-1 Gag RNA Is Optimized by Evaluating Alternative Length Formats

Silencing of HIV-1 gag gene from epidemic strains among men who have sex with men (MSM) in Tianjin, China by a broad-spectrum short hairpin RNA

A novel antiviral approach

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