siPOOLs siRNA Pools

siPOOLs

Potent & Specific Gene Knock-down by RNAi


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Exceptional gene silencing specificity for reliable phenotypes


siRNA pools (siPOOLs) are high complexity pools of 30 optimally-designed siRNAs that were demonstrated to efficiently remove off-target effects and improve reliability of results (Hannus et al., 2014). Our Pack Hunter (pooling) approach counters off-targeting of individual siRNAs by diluting their concentrations below thresholds that stimulate phenotypes. With proprietary design algorithms, siRNA sequences within siPOOLs are also optimized for maximal transcript coverage, efficient hybridization and filtered against paralogues, enabling highly efficient and specific gene silencing.


Benefits of using siPOOLs


Benefit of siPOOLs: Simple and fast to use Simple & fast to use
enefit of siPOOLs: High specificity Highly specific
enefit of siPOOLs: Consistent phenotypes Consistent phenotypes

Benefit of siPOOLs: Validation-inclusive guarantee Validation-inclusive guarantee
Benefit of siPOOLs: Customized design using latest annotations Customized design using latest annotations
Benefit of siPOOLs: HPLC-purified and non-toxic HPLC-purified and non-toxic

 


Key Problem: Off-target effects of siRNAs

Scientists have been using RNA interference (RNAi) as a rapid and efÔ¨Ācient tool to establish gene function. Yet the off-target effects and variable performance of short interfering RNAs (siRNAs) remain a troubling drawback, consuming precious time and resources in validation efforts.

Leading Cause: miRNA-like transcript downregulation


siRNAs typically bind with full complementarity to target RNA transcripts, guiding their degradation by the RNAi machinery. Off-target effects are largely caused by siRNAs mimicking endogenous gene regulators, micro RNAs (miRNAs). As miRNAs require only a 6 base seed match to 3' untranslated regions (UTR) to trigger transcript downregulation, siRNAs can alter the expression of numerous unintended targets when processed via this mechanism.

How siPOOLs Improve Specificity


How siPOOLs Improve Specificity

Individual siRNAs or low complexity siRNA pools containing 3-4 siRNAs often hit multiple off-target genes and exhibit variable target gene knock-down.
Short interfering RNA (siRNA) pools, siPOOLs are highly complex and defined pools of 30 siRNAs, each siRNA present at picomolar working concentrations. This:
  • Dilutes the off-target signature of each siRNA, increasing on-target specificity.
  • Ensures co-operative knock-down of the target gene, producing more robust and reliable results.


 


Optimized and detailed siRNA design

With defined siRNA sequences within the siPOOL, targeting can be optimized against specific transcript isoforms or closely related genes. Proprietary siRNA design algorithms select the most potent siRNAs based on thermodynamic properties that favour guide strand loading into the RNA-induced silencing complex (RISC) (refer Technote 2 for more details on siPOOL design). Using latest RefSeq annotations and genome-wide paralogue filtering, siPOOLs are designed for maximum coverage of all targeted transcripts with high specificity.


 


Webinar: Dealing with RNA interference and the siPOOL concept



 


World leading scientist publish with siPOOLs

Kerstin D√∂rner et al. (2022) Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism Nucleic Acids Research

Falke et al. (2022) Knockdown of the stem cell marker Musashi-1 inhibits endometrial cancer growth and sensitizes cells to radiation Stem Cell Research & Therapy

Lechner et al. (2022) Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target Nature Chemical Biology

Read more publications on siPOOLs


 


For further information:



 

Supporting Data

Download siPOOL Brochure

 
 


Advantages of siPOOLs



Simple and fast to use

siPOOLs are compatible with a wide-range of transfection reagents and results are seen within days.

Highly specific and efficient

siPOOLs reduce off-targeting by 5-25 fold and achieve ‚Č• 70% gene knock-down at 1-3 nM in standard cell lines.

Consistent phenotypes

Phenotypes produced by sequence-independent siPOOLs are highly correlated as opposed to siRNAs.


Validation-inclusive Guarantee

siPOOL validation by rtqPCR is performed with possibility of re-design if less than 70% knock-down is seen under optimal transfection.

Customized design using latest annotations

Detailed design ensures optimized thermodynamics and paralog avoidance. Sequence info available.

HPLC-purified and non-toxic

All siPOOLs are HPLC-purified reducing risk of contaminants and side-effects.


 


Optimized and Detailed siRNA Design



With defined siRNA sequences within the siPOOL, targeting can be optimized against specific transcript isoforms or closely related genes. Proprietary siRNA design algorithms select the most potent siRNAs based on thermodynamic properties that favour guide strand loading into the RNA-induced silencing complex (RISC) (refer Technote 2 for more details on siPOOL design). Using latest RefSeq annotations and genome-wide paralogue filtering, siPOOLs are designed for maximum coverage of all targeted transcripts with high specificity.

siPOOLs




 

Higher specificity with siPOOLs

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siRNA
siPOOL


Specific reagents should only affect their target.

Expression profiling by microarray in HeLa cells revealed a single siRNA can induce numerous off-target genes (red dots) while a siPOOL against the same target gene (green dot), and containing the non-specific siRNA, had greatly reduced off-target effects.



Better reproducibility and potent knock-down efficiency with siPOOLs

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siRNA
siPOOL
siPOOL


siRNAs vary strongly in their knock-down efficiency.

siPOOLs against the same gene gave similar knock-down efficiencies compared to single siRNAs, indicating greater robustness and reproducibility (left and middle panel: correlation plots of real-time quantitative PCR measurements of target RNA levels).

siPOOLs also exhibit potent gene knock-down. In commonly used cell lines, gene knock-down efficiencies of 75-98% are often achieved at 1 nM concentrations for many genes (right panel).




Phenotypes you can trust with siPOOLs

blue line


siRNA
siPOOL


If reliable and specific, two reagents that target the same gene should produce similar phenotypes.

We screened 36 genes using two siPOOLs per gene from our human kinase siPOOL library and three siRNAs per gene from a commercially available library and measured cell viability in A549 cells. Only siPOOLs produced consistent phenotypes.

For a complete publication on siPOOLs:

Hannus M. et. al. siPOOLs: highly complex but accurately defined siRNA pools eliminate off-target effects. Nucleic Acids Res. (2014)

 


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