Dharmacon has been the company of choice for siRNA since the 1990’s and has been improving methods of synthesizing siRNA ever since. Researchers that work with siRNA know that the 2 major factors within your control which are critical for getting an siRNA to work are siRNA design and delivery. Dharmacon helps you out by constantly developing improved algorithms and developing modifications to improve specificity and silencing efficiency. The most recent example is their new ON-TARGET™ Plus technology that increases siRNA specificity for targeting your gene of interest. They also have a free guide to siRNA techniques on their website that is called the
RNAi Technical Reference and Application Guide. Of course, you have to give your contact information and then wait 2-4 weeks to get it, but it is worth it, especially if you are new to the technique. Their major competitor, Ambion, also has a useful guide on their website called
RNA Interference Research Guide that is immediately available for free download.
What sets Dharmacon’s services apart from their competitors is their cost-effective and quick synthesis of custom siRNAs and their cutting edge modifications for siRNA stability and specificity. They provide a variety of purification and synthesis services to keep costs down. This makes them the company of choice for synthesis of siRNA when you already know the sequence you want and if you have the ability to purify siRNA on your own. If you don’t know a working sequence for your gene of interest, they also have an extensive database of predesigned siRNAs and SmartPool siRNAs. SmartPool siRNAs have 4 different company designed siRNAs pooled together to maximize the chance of the siRNA working. Unfortunately, these are very expensive, and you have to pay extra to get the sequences so you can have more synthesized later.
When comparing siRNA synthesis companies, it is important to consider the scale and purification. Most people will want to order their siRNA in working condition, meaning duplexed and at least PAGE purified. This translates to service option ‘B’ for Dharmacon. However, if you are comfortable PAGE- or HPLC-purifying your own siRNA, order the least expensive synthesis option, ‘A’. Dharmacon provides simple protocols for annealing, desalting, and deprotecting the siRNA. We have performed these according to Dharmacon’s protocols in our lab and found them to be straightforward.
Our lab uses Dharmacon for all our custom siRNA synthesis. We use siRNA sequences that have been previously published and order on the smallest scale to test them. In every case, the FAXed ordering was smooth and simple. Our custom siRNA arrived in about 2 weeks. Dharmacon also included nuclease-free water and 5x siRNA dilution buffer with an easy to follow protocol for dilution to the required working concentration. There has only been 1 case out of 6 where a published sequence did not work for us. In that case, we designed a second sequence ourselves that worked on the first try.
We also had several cases where there was no published siRNA sequence for a gene. However, Dharmacon’s predesigned siRNA prices were out of reach for our budget (we have many genes to target), so we took a more cost effective route to find working sequences for these genes. First, we used the Ambion’s free Target Finder on their website to help choose potential target sequences. Then we purchased Ambion’s Silencer siRNA Transcription Kit, for making up to 15 small scale siRNA preps. We used this kit to make 3 siRNAs per gene in order to find one that worked well before ordering a custom synthesis from Dharmacon. Similar kits are available from other companies for competitive prices.
We also use Dharmacon’s siGlo fluorescently labeled control siRNA for determining delivery efficiency in different cell lines. This control is easily detectable by flow cytometry and allows you to optimize siRNA transfection efficiencies within a day.
Our experiences with Dharmacon have been smooth and very good. We hope their predesigned siRNA prices will drop as they recover their R&D costs so that academic labs can make more use of this excellent technology.
Rebecca A. MacCorkle, PhD
Postdoctoral Fellow
Baylor College of Medicine
Department of Molecular & Cellular Biology