siGENOME siRNA Reagents

Trusted for high-confidence silencing since 2002

Expert siRNA design and guaranteed gene silencing provide a value-priced option for high quality RNAi results. Predesigned siGENOME siRNA are available as individual reagents and in SMARTpool format.

PAK1 ( Human )

Entrez Gene 5058 entrezgene 5058

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p21 (RAC1) activated kinase 1

Alias

PAKalpha

This gene encodes a family member of serine/threonine p21-activating kinases, known as PAK proteins. These proteins are critical effectors that link RhoGTPases to cytoskeleton reorganization and nuclear signaling, and they serve as targets for the small GTP binding proteins Cdc42 and Rac. This specific family member regulates cell motility and morphology. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010].

Straightforward and reliable gene knockdown

siGENOME siRNA reagents are widely recognized and trusted for highly efficient target gene silencing. Our scientists were the first to establish siRNA design rules for high potency silencing and continue to drive innovation in this area. By providing genome-wide siRNAs designed with the SMARTselection algorithm, researchers can focus on successful RNAi experiments instead of optimizing siRNA designs for their genes of interest.

siGENOME siRNA is available as pre-designed, genome-wide SMARTpool and individual siRNA reagents for human, mouse and rat. Simply search for your gene of interest and choose from the available product formats and quantities.

Guaranteed knockdown by SMARTpool and 3 of 4 individual siRNAs (see Guarantee tab)
Antisense strand loading into RISC ensured by thermodynamic analysis and selective application of a sense strand-blocking modification
Sequence information provided with siRNA purchase

Design and modification strategies for optimal silencing

In addition to identifying potent siRNA designs with the SMARTselection algorithm, the creation of siGENOME siRNAs also involves:

Thermodynamic analysis to determine optimal antisense strand-loading characteristics for effective silencing
BLAST analysis of both strands to alleviate cross-targeting

To retain more high-scoring siRNA designs, the above analysis may trigger the use of a sense strand-blocking modification to ensure only the appropriate strand enters RISC for effective target knockdown (see Figure 2, Supporting Data).

Product Formats

SMARTpool: A mixture of 4 siRNA provided as a single reagent; providing advantages in both potency and specificity.
Set of 4: A convenient option for purchasing aliquots of all 4 individual siRNAs targeting a single gene.
Individual siRNAs: Select 1, 2, 3 or 4 individual siRNAs per gene.

Order Quantity Guidelines

siGENOME reagents are routinely used at 5 to 25 nM concentration. The calculations below, based on 25 nM, are for estimation purposes only and assume no loss from pipetting.

	Approximate # reactions (wells) at 25 nM siRNA concentration
nmol	96-well plate(100 µL total reaction volume)	24-well plate(500 µL total reaction volume)	12-well plate(1000 µL total reaction volume)
1	400	80	40
2	800	160	80
5	2000	400	200
10	4000	800	400
20	8000	1600	800

Custom siRNA design

Design and order custom siRNA sequences using our siDESIGN center.

A robust selection of validated positive, negative, and novel RISC-Free® controls to effectively assess all aspects of RNAi experiments. Controls are critical for the successful application of RNAi. Including the appropriate controls in each experiment adds certainty to the cause-and-effect relationship between gene silencing and siRNA, and aids in the distinction between target-specific and potential off-target effects.

Select a species-specific positive control to silence an expressed housekeeping gene in your experimental cell type. Our panel of non-targeting controls permits assessment of potential non-specific effects, to find the optimal negative control for your cell type, and your assay.

siGENOME Positive Control Reagents	Species	Catalog Number
siGENOME Cyclophilin B Control siRNA	Human, Mouse, Rat	D-001136-01
siGENOME GAPD Control siRNA	Human	D-001140-01
siGENOME Lamin A/C Control siRNA	Human, Mouse, Rat	D-001050-01
siGENOME Negative Control Reagents	Species	Catalog Number
siGENOME Non-targeting siRNAs	Human, Mouse, Rat	D-001210-0X
siGENOME Non-targeting siRNA Pools	Human, Mouse, Rat	D-001206-13
siGENOME RISC-Free siRNA	Human, Mouse, Rat	D-001220-01
siGENOME Control siRNA Kits	Species	Catalog Number
siGENOME Controls Basic Kit	Human, Mouse, Rat	K-002800-C4-01
siGENOME Controls Complete Kit	Human, Mouse, Rat	K-002800-C2-0X

siGENOME SMARTpool reagents demonstrate potency at 5 nM working concentration

A comparison of target gene silencing at 5 and 100 nM concentration illustrates the high potency of siGENOME SMARTpool reagents. 5 or 100 nM siGENOME SMARTpool siRNA reagents targeting the indicated genes was transfected into HeLa cells (10K cells/well) using 0.1 μL/well DharmaFECT 1. The negative control (NTC pool) was siGENOME Non-Targeting Pool #2.

Unnecessary sense-strand inactivation can increase off-target activity

Unmodified and sense strand-inactivated siRNAs were used to target five genes. In four cases off-targets were increased due to enhanced RISC loading of the antisense strand when the sense strand was modified. The unmodified siRNAs have natural guide-strand loading characteristics. All siRNAs had comparable silencing potency. Data shown represents genes down-regulated by twofold or more. HEK293 cells were transfected with 100 nM siRNA using 0.2 μL of DharmaFECT 1. Data was analyzed at 24 hours by genomewide microarray analysis (Agilent).

Why not modify ALL siGENOME siRNAs to ensure proper strand loading? It has been demonstrated by Dharmacon scientists¹ and others² that forcing antisense (guide) strand entry into RISC may actually INCREASE off-targets due to increased loading of the guide strand and resulting off-target activity by its seed region. siGENOME siRNAs are designed with thermodynamic properties to naturally facilitate guide strand entry to RISC, which has been demonstrated to correlate with functionality¹. However, in cases where a high-scoring siGENOME siRNA does not possess ideal strand-loading characteristics, a sense (passenger) strand-inhibiting chemical modification (ON-TARGET) is utilized to promote guide strand entry. Approximately 20% of siGENOME siRNAs carry the ON-TARGET modification.

Microarray analysis demonstrates SMARTpool potency and reduced off-targets

Target gene silencing is maintained while off-target signatures are reduced with a SMARTpool siRNA reagent when compared to its four constituent siRNAs.

Total RNA for microarray extracted from HeLa cells 24 hours post-transfection. Green indicates mRNA reduced by two-fold or more (Agilent 22K Platform).