LNA(R) incorporated siRNAs exhibit lower off-target effects compared to 2'-OMethoxy in Cell Phenotypic Assays and Microarray Analysis | Zendy

Nitin Puri | Zendy; Xin Wang | Zendy; Rajeev Varma | Zendy; Cleo Burnett | Zendy; Lilia M. Beauchamp | Zendy; D. Batten | Zendy; Megan M. Young | Zendy; Veronica Sule | Zendy; Keith E. Latham | Zendy; Timothy J. Sendera | Zendy; Christophe J. Echeverri | Zendy; Christoph Sachse | Zendy; Susan Magdaleno | Zendy

Open Access

LNA(R) incorporated siRNAs exhibit lower off-target effects compared to 2'-OMethoxy in Cell Phenotypic Assays and Microarray Analysis

Author(s) -

Nitin Puri,

Xin Wang,

Rajeev Varma,

Cleo Burnett,

Lilia M. Beauchamp,

D. Batten,

Megan M. Young,

Veronica Sule,

Keith E. Latham,

Timothy J. Sendera,

Christophe J. Echeverri,

Christoph Sachse,

Susan Magdaleno

Publication year - 2008

Publication title -

nucleic acids symposium series

Language(s) - English

Resource type - Journals

eISSN - 1746-8272

pISSN - 0261-3166

DOI - 10.1093/nass/nrn013

Subject(s) - small interfering rna , locked nucleic acid , rna interference , microarray , phenotype , microarray analysis techniques , biology , microbiology and biotechnology , nucleic acid , gene , computational biology , rna , gene expression , genetics

Despite the promise of short interfering RNAs (siRNA), contending with off-target is a challenge for RNAi users. To alleviate these problems, we have developed locked nucleic acid (LNA) modified siRNAs and optimized performance using cellular phenotypic assays as well as microarray analysis. During development, we compared LNA and 2'OMethoxy (2'OMe) chemistries placed strategically throughout the siRNA molecule and found a novel pattern of LNA placement that greatly improved the specificity of the siRNA and reduced it's toxicity in culture while preserving the potency of the siRNA. The improvements in specificity made by LNA-modified siRNAs were developed and validated by measuring the phenotypic signatures in a high content cell-based screening assay as well as comparison of the level of differentially expressed genes observed in microarray analysis between modified and unmodified siRNAs. HT screening of a collection of genes demonstrated that the LNA-modified siRNAs exhibits the best overall rate to elicit the expected phenotype, reduced toxicity and achieved an improved coherence of phenotype compared to 2'OMe-modified or unmodified siRNAs.

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