Improved siRNA/shRNA Functionality by Mismatched Duplex | Zendy

Haoquan Wu | Zendy; Hongming Ma | Zendy; Chunting Ye | Zendy; Danielle Ramirez | Zendy; Shuiping Chen | Zendy; Jessica Montoya | Zendy; Premlata Shankar | Zendy; Xiaozhong A. Wang | Zendy; N. Manjunath | Zendy

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Improved siRNA/shRNA Functionality by Mismatched Duplex

Author(s) -

Haoquan Wu,

Hongming Ma,

Chunting Ye,

Danielle Ramirez,

Shuiping Chen,

Jessica Montoya,

Premlata Shankar,

Xiaozhong A. Wang,

N. Manjunath

Publication year - 2011

Publication title -

plos one

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.99

H-Index - 332

ISSN - 1932-6203

DOI - 10.1371/journal.pone.0028580

Subject(s) - small interfering rna , small hairpin rna , gene silencing , rna interference , microrna , trans acting sirna , oligonucleotide , rna , microbiology and biotechnology , duplex (building) , computational biology , biology , rna silencing , chemistry , gene , genetics , dna

siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity.

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