Designing effective siRNAs with off-target control.
Successful gene silencing by RNA interference requires a potent and specific depletion of the target mRNA. Target candidates must be chosen so that their corresponding short interfering RNAs are likely to be effective against that target and unlikely to accidentally silence other transcripts due to sequence similarity. We show that both effective and unique targets exist in mouse, fruit fly, and worm, and present a new design tool that enables users to make the trade-off between efficacy and uniqueness. The tool lists all targets with partial sequence similarity to the primary target to highlight candidates for negative controls.
Snøve
Ola
O
Interagon AS, Medisinsk teknisk senter, NO-7489 Trondheim, Norway. ola.snove@interagon.com
Nedland
Magnar
M
Fjeldstad
Ståle H
SH
Humberset
Håkon
H
Birkeland
Olaf R
OR
Grünfeld
Thomas
T
Saetrom
Pål
P
D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans; D004331:Drosophila melanogaster; D018390:Gene Targeting / Q000379:methods*; D005818:Genetic Engineering / Q000379:methods; D051379:Mice; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D034741:RNA, Small Interfering