Reducing off-target effects in RNA interference experiments

The success of functional genomic studies using RNA interference (RNAi) technology can be limited by non-specific effects of the siRNA reagents. ON-TARGETplus™ siRNA reagents from Dharmacon™ are designed to knock down the target gene with minimal off-target effects. You can use these reagents in your gene silencing experiments to reduce the presence of off-target phenotypes without jeopardizing on-target gene knockdown, writes Dr. Christian Nievera, senior product manager for RNAi and functional genomics screening libraries at Horizon Discovery.

The use of small interfering RNAs (siRNAs) for silencing gene expression has become an invaluable tool in numerous fields of scientific research. However, experiments using this technology can be complicated by off-target effects, manifesting as measurable phenotypes such as false positives. These non-specific effects are difficult to predict and analyze and can confound the interpretation of experimental data.

Scientists from Dharmacon have recognized this issue, we have extensively reviewed the evidence relating to off-target effects. Three strategies have been identified that are proven to improve the specificity of siRNA effects. These three strategies are incorporated into the Dharmacon ON-TARGETplus siRNA reagents to ensure cleaner experimental results in loss-of-function assays.

1. Pool siRNAs

Off-target effects are reduced when a lower concentration of siRNA is used. However, reducing the concentration would normally be associated with a depletion of target gene knockdown. Dharmacon offers a simple solution: SMARTpool siRNA reagents pool four highly functional SMARTselection-designed siRNAs targeting the same gene. Using SMARTpool siRNA considerably reduces the off-target profile without sacrificing target-specific knockdown.

2. Chemically modify siRNAs

Scientists at Dharmacon have identified a unique combination of modifications that eliminate as much as 80% of the off-target activity. These chemical modifications reduce both sense and antisense strand off-target effects while preserving on-target knockdown.

3. Apply design filters

Certain siRNA design features, such as the presence of multiple 3’ UTR seed matches, have been associated with the likelihood of a gene being off-targeted. The use of novel rational design filters, incorporating an understanding of features known to affect the specificity of siRNA binding, has enabled Dharmacon to optimize its siRNA reagents. ON-TARGETplus siRNA reagents have been developed using pooling strategies, chemical modifications, and design filters to reduce off-target activity versus unmodified siRNA without jeopardizing on-target gene knockdown.

Avoid unintended gene modulation and have confidence in the specificity of your RNAi by using ON-TARGETplus siRNA reagents in your functional genomic studies.

For more information on siRNA reagents from Dharmacon, contact Horizon Discovery >>