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Does any one have a target gene knockdown with negative control siRNA?

Does any one have a target gene knockdown with negative control siRNA? - RNAi and SiRNA Forum

Does any one have a target gene knockdown with negative control siRNA? - Discuss and Post Questions in this forum about RNA interference and siRNA. RNAi and siRNA transfection, inhibition of endogenous genes, and miRNA and shRNA.


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Old 07-24-2010, 05:59 PM
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Default Does any one have a target gene knockdown with negative control siRNA?



Hi,

I have siRNA for gene A and looking for it's effects on gene B. My siRNA has knock down almost 80% of the trageted gene and affected the expression of gene B. But somehow my negative control (non-targeting) siRNA is effecting the gene B expression with out any knock down of gene A. Has any one seen this before? Could anyone has suggestion in this matter.

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Old 08-03-2010, 04:42 PM
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Default Re: Does any one have a target gene knockdown with negative control siRNA?

Off-target modulation of gene expression is a usual side effect of siRNA.

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Off-Target Analysis of Control siRNA Molecules Reveals Important Differences in the Cytokine Profile and Inflammation Response of Human Fibroblasts. Baum P, Fundel-Clemens K, Kreuz S, Kontermann RE, Weith A, Mennerich D, Rippmann JF. Oligonucleotides. 2009 Dec 28. [Epub ahead of print]

Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Alló M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, Klinck R, Chabot B, Kornblihtt AR. Nat Struct Mol Biol. 2009 Jun 21. [Epub ahead of print]

Specific and effective gene knock-down in early chick embryos using morpholinos but not pRFPRNAi vectors. Mende M, Christophorou NA, Streit A. Mech Dev. 2008 Nov-Dec;125(11-12):947-62. Epub 2008 Sep 3.

Widespread changes in protein synthesis induced by microRNAs. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Nature. 2008 Sep 4;455(7209):58-63. Epub 2008 Jul 30.

Comparison of siRNA-induced off-target RNA and protein effects. Aleman LM, Doench J, Sharp PA. RNA. 2007 Mar;13(3):385-95. Epub 2007 Jan 19.

Morpholino, siRNA, and S-DNA Compared: Impact of Structure and Mechanism of Action on Off-Target Effects and Sequence Specificity. Summerton J. Med Chem. 2007;7(7):651-660

Retraction of synapses and dendritic spines induced by off-target effects of RNA interference. Alvarez VA, Ridenour DA, Sabatini BL. J Neurosci. 2006 Jul 26;26(30):7820-5.

3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A. Nat Methods. 2006 Mar;3(3):199-204.

Nonspecific, concentration-dependant stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). Persengiev SP, Zhu X and Green M. RNA 2004; 10:12-18.

Transcriptional gene silencing by short interfering RNAs. Kawasaki H, Taira K. Curr Opin Molec Therap. 2005 7(2):125-31.

Small interfering RNA-induced transcriptional gene silencing in human cells. Morris KV, Chan SWL, Jacobson SE, Looney DJ. Science 2004 Aug 27;305(5688):1289-92. Epub 2004 Aug 5.

A rapid and sensitive assay for quantification of siRNA efficiency and specificity. Smart N, Scambler PJ, Riley PR. Biol Proced Online. 2005;7:1-7. Epub 2005 Jan 24.

Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1892-7. Epub 2004 Feb 09.

Noise amidst the silence: off-target effects of siRNAs? Jackson AL, Linsley PS. Trends Genet. 2004 20(11):521-4

Expression profiling reveals off-target gene regulation by RNAi. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS. Nat Biotechnol. 2003 Jun;21(6):635-637.

Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation: Implications for off-target activity of small inhibitory RNA in mammalian cells. Saxena S, Jonsson ZO, Dutta A. J Biol Chem. 2003 Nov 7;278(45):44312-44319.
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