Minimal-length short hairpin RNAs: The relationship of structure and RNAi activity
| Autor: | Pavan Kumar, Heini Ilves, Joshua Shorenstein, Qing Ge, Sergei A. Kazakov, Anne Dallas, Brian H. Johnston |
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| Rok vydání: | 2009 |
| Předmět: |
Ribonuclease III
Base Pair Mismatch Base pair Efficiency Models Biological Article Substrate Specificity law.invention DEAD-box RNA Helicases Structure-Activity Relationship law RNA interference Catalytic Domain Humans Nucleotide RNA Small Interfering Molecular Biology Cells Cultured chemistry.chemical_classification Base Sequence biology fungi Molecular biology Cell biology chemistry Sense strand biology.protein Recombinant DNA Nucleic Acid Conformation RNA Interference Interferons Dimerization Dicer |
| Zdroj: | RNA. 16:106-117 |
| ISSN: | 1469-9001 1355-8382 |
| Popis: | Small hairpin RNAs (shRNAs) are widely used in RNAi studies and typically consist of a stem of 19–29 base pairs (bp), a loop of at least 4 nucleotides (nt), and a dinucleotide overhang at the 3′ end. Compared with shRNAs with 21–29 bp stems, we have found that shRNAs with 19-bp or shorter stems (sshRNAs) possess some unique structure–activity features that depend on whether the antisense strand is positioned 5′ or 3′ to the loop (L- or R-type sshRNAs, respectively). L sshRNAs can have IC50s in the very low picomolar range, and sshRNAs with nominal loop sizes of 1 or 4 nt were at least as active as those with longer loops. L sshRNAs remained highly potent even when the 3′ end of the antisense strand was directly linked with the 5′ end of the sense strand. In this case, the sense strand can be shorter than the antisense strand, and the loop can be formed entirely by the 3′ end of the antisense strand. Monomer sshRNAs are not processed by recombinant Dicers in vitro. Although they can form dimers that are sometimes Dicer substrates, their RNAi activity is not dependent on the formation of such structures. Our findings have implications for the mechanism of action of sshRNAs, and the ability to design highly potent shRNAs with minimal length is encouraging for the prospects of the therapeutic use of direct-delivered shRNAs. |
| Databáze: | OpenAIRE |
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