Susan Magdaleno Describes Silencer® Select siRNA Technology
by Jennifer Hornstein - 06/11/12
Meet the Inventor
Susan Magdaleno is a Senior Staff Scientist in the research and development department at Ambion, which is a part of Life Technologies. Susan was asked to describe Silencer® Select siRNA Technology. Below is a recap of her reply.
Back when siRNAs were discovered as a technology that can be used for general applications in the lab, there were two main pain points.
1. One was the efficiency of siRNA design. We have some basic rules around how to get an siRNA that gave pretty good efficiency. But it was really dependent on the gene target of interest and sometimes you have to use very high concentration levels to get that level of knockdown that is needed for biological applications. So potency was a big issue.
2. The other one, which is a little more difficult to overcome, was the idea around siRNA specificity. We could get good designs, but sometimes they knocked down more than the target of interest, i.e. cleaved other mRNAs with partial sequence homology. As a result we ended up with some very confusing biology. Were we knocking down just the RNA of interest, or were there off-target effects?
The combination of off-target effects and issues around potency and efficiency really caused a lot of pain points in functional analysis of mRNA using the siRNAs as a silencing technology.
The main benefits of Silencer® Select Technology are two fold
1. One is the ability to use it at very low concentrations, so part of the development also included using a new algorithm called a Support Vector Machine (SVM) algorithm. It allows for classifying two things either as good or bad. So we're not really aligning things along a linear range, which is complicated, we're classifying things as good or bad. And dependent upon where we put that threshold, we can classify things as we like.
We decided to only look for siRNAs that gave 90% knockdown or better. So the Support Vector Machine really allowed to differentiate super-high potency siRNAs and then everything else. Thus one of the benefits of Silencer® Select is the efficiency of the design. We are close to 100% of the siRNA designs resulting in at least 80% knockdown of the corresponding mRNA targets. Very high efficiency across all different designs!
2. The other benefit for Silencer® Select siRNAs is the reduced off-target effects. We've got chemical modifications onto the siRNAs that drive the uptake of the correct strand of the siRNA into RISC. This really enforces the utilization of the guide strand and eliminates any application on the passenger strand within RISC complex. Additionally, we don't understand the mechanism yet, but it eliminates off-target effects and really drives the cleaner phenotypes in cell-based assays. And it does it in a way that does not impact the potency of the siRNA. So we can eliminate the off-target effects, but maintain the siRNA high potency.
Silencer® Select is fairly unique on the market. It's the only siRNA product that contains Locked Nucleic Acid modifications (LNA). These are our third generation oligonucleotide modifications that really alter the melting temperature of the oligo and conformation of the duplex. The way we've introduced the LNAs in unique positions within the siRNA results in more efficient interaction with the RISC, and it drives the interaction with the mRNA target in a more specific way.
Learn more about siRNA Technology.