Navigation Links
Selecting siRNA Sequences to Incorporate into the pSilencer Vectors

The first step in preparing a plasmid for siRNA experiments is to identify target sequences in the gene of interest that are susceptible to siRNA-induced degradation. We have found that a little more than half of the siRNAs provide at least a 50% reduction in target mRNA levels and approximately 1 out of 4 siRNAs provide a 75-95% reduction. The general process begins with scanning the length of the target gene for potential siRNA target sites. For siRNA expression vectors, the target sites should have 5' terminal AAs because, upon folding the siRNAs hairpins will give rise to UU overhangs. These UU overhangs will therefore be complementary to the AA in the target site. The 21 nucleotide siRNA target sequences are then compared to an appropriate genome database to eliminate sequences with significant homology to other genes. For screening, we typically test four siRNAs per target. We space the siRNAs down the length of the gene sequence to reduce the chances of targeting a region of the mRNA that is either highly structured or bound by regulatory proteins.

Constructing four siRNA expression plasmids for each target can be time-consuming and expensive. In vitro transcription provides a less formidable siRNA screening method. To ensure that siRNAs expressed from plasmids are functionally equivalent to siRNAs prepared by in vitro transcription, we prepared plasmids and siRNAs targeting four different sequences in the cyclophilin and GAPDH genes. These nucleic acids were transfected into HeLa cells. Silencing was evaluated by Northern analysis using probes specific to GAPDH, cyclophilin, and 28S rRNA. The hybridiz ation signal from the various targets was quantitated by phosphorimager. As seen in Figure 1, the susceptibility of siRNA target sites to siRNA-mediated gene silencing appears to be comparable for both in vitro prepared siRNAs and RNA Pol III-expressed siRNAs. This is also true for chemically synthesized siRNAs versus RNA Pol III-expressed siRNAs. Therefore, it is not necessary to re-screen genes for which functional siRNAs have already been identified.

Transcribed siRNA siRNAVector GAPDH None 100% 100% 5' 25% 17% 5' Medial 7% 13% 3' Medial 36% 20% 3' 45% 63% Cyclophilin None 100% 100% 5' 5% 23% 5' Medial 15% 19% 3' Medial 45% 29% 3' 70% 54%

Figure 1. Correlation of Target Site Selection Between siRNA Generated In Vitro and In Vivo. siRNAs to four target sites in each of two genes (GAPDH and cyclophilin) were selected and prepared using the Silencer siRNA Construction Kit. Sequences encoding hairpin siRNAs to the same target sequences were sub-cloned into pSilencer 2.0-U6 and 3.0-H1. The siRNAs and siRNA expression vectors were transfected into HeLa cells using siPORT-Lipid (Ambion). Target RNA levels were assessed post-transfection (48 hr) by Northern analysis using the NorthernMax procedure (Ambion). The relative levels of the target genes were measured against cells transfected with negative control siRNA or negative control siRNA expression vector.

back to top

Ordering Information
Cat# Product Name Size 1620 Silencer siRNA Construction Kit 15 siRNA synthesis rxns 7207 pSilencer 1.0-U6 (circular) 20 g 7208 pSilencer 1.0-U6 (linear) 20 rxns 7209 pSilencer 2.0-U6 20 rxns 7210 pSilencer 3.0-H1 20 rxns


Page: All 1 2 3 4

Related biology technology :

1. Custom and library siRNA for efficient gene silencing
2. Custom and library siRNA for efficient gene silencing
3. Cancer siRNA Oligo Set Version 1.0
4. Library siRNA
5. Custom siRNA Oligo Synthesis Service
6. Efficient RNAi-mediated gene silencing in neuronal cells using QIAGEN siRNA and TransMessenger Transfection Reagent*
7. Quantification of siRNA Silencing Efficiency Using the LightCycler System
8. Housekeeping Genes: Universal Positive Controls in siRNA Knockdown Experiments
9. Confirming gene silencing mechanism by pGFP/GFP22 siRNA co-transfection
10. siRNA transfection optimization with the Agilent 2100 bioanalyzer
11. siRNA Design Guidelines
Post Your Comments:

(Date:11/25/2015)... Nov. 25, 2015  PharmAthene, Inc. (NYSE MKT: PIP) ... a stockholder rights plan (Rights Plan) in an effort ... carryforwards (NOLs) under Section 382 of the Internal Revenue ... PharmAthene,s use of its NOLs could be substantially ... defined in Section 382 of the Code. In general, ...
(Date:11/25/2015)... ANGELES and HOLLISTON, Mass. ... Technology, Inc. (Nasdaq: HART ), a biotechnology company ... that CEO Jim McGorry will present at ... December 1, 2015 at 2:30 p.m. PT. The presentation ... below) for 30 days. Management will also be available ...
(Date:11/25/2015)... ... November 25, 2015 , ... ... Organization of Black Aerospace Professionals (OPBAP) has been formalized with the signing of ... team leaders met with OPBAP leaders Capt. Karl Minter and Capt. Albert Glenn ...
(Date:11/25/2015)... ... November 25, 2015 , ... Jessica Richman and Zachary Apte, ... their initial angel funding process. Now, they are paying it forward to other ... stage investments in the microbiome space. In this, they join other successful ...
Breaking Biology Technology:
(Date:11/9/2015)... , Nov. 9, 2015  Synaptics Inc. (NASDAQ: ... today announced broader entry into the automotive market with ... match the pace of consumer electronics human interface innovation. ... are ideal for the automotive industry and will be ... Europe , Japan ...
(Date:10/29/2015)... JOLLA, Calif. , Oct. 29, 2015  The ... a new report titled, "DNA Synthesis and Biosecurity: Lessons ... well the Department of Health and Human Services guidance ... issued in 2010. --> ... but it also has the potential to pose unique ...
(Date:10/29/2015)... October 29, 2015 NXTD ... company focused on the growing mobile commerce market ... that StackCommerce, a leading marketplace to discover and ... Wocket® smart wallet on StackSocial for this holiday ... or the "Company"), a biometric authentication company focused ...
Breaking Biology News(10 mins):