Many commonly used siRNAs risk off-target activity.

Abstract:

:Using small interfering RNA (siRNA) to induce sequence specific gene silencing is fast becoming a standard tool in functional genomics. As siRNAs in some cases tolerate mismatches with the mRNA target, knockdown of genes other than the intended target could make results difficult to interpret. In an investigation of 359 published siRNA sequences, we have found that about 75% of them have a risk of eliciting non-specific effects. A possible cause for this is the popular BLAST search engine, which is inappropriate for such short oligos as siRNAs. Furthermore, we used new special purpose hardware to do a transcriptome-wide screening of all possible siRNAs, and show that many unique siRNAs exist per target even if several mismatches are allowed. Hence, we argue that the risk of off-target effects is unnecessary and should be avoided in future siRNA design.

authors

Snøve O Jr,Holen T

doi

10.1016/j.bbrc.2004.04.175

subject

Has Abstract

pub_date

2004-06-18 00:00:00

pages

256-63

issue

1

eissn

0006-291X

issn

1090-2104

pii

S0006291X04009428

journal_volume

319

pub_type

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