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siRNA Design - Choosing your siRNA

What overhangs does Sigma use on their MISSION® Predesigned siRNA, and why are those overhangs chosen?
We use dTdT overhangs. According to Elbashir et al. 2001*, "The thymidine overhang was chosen because it may enhance nuclease resistance of siRNAs in the cell culture medium and within transfected cells."
It seems that pretty early on in RNAi research, the leaders in the field were choosing dTdT overhangs, so it may in some ways be a historic choice. siRNAs are often designed with dTdT overhangs, but UU or UG overhangs are also not uncommon. Several Elbashir et al. papers from 2001 outline a set of rules for siRNA design based on a limited number of genes and systems, but researchers continue to use dTdT overhangs as well as UU overhangs.
*Elbashir, S.M., et al., Duplexes of 21-nucleotide RNAs mediate RNA interference in mammalian cell culture. Nature 411(6836), 494-8 (2001). (link to PMID 11373684)
How does your Rosetta algorithm work?
The Rosetta siRNA Design Algorithm utilizes Position-Specific Scoring Matrices (PSSM) and knowledge of the all-important siRNA seed region to predict the most effective and specific siRNA sequences for your target gene of interest. Additionally, the Rosetta siRNA Design Algorithm has been trained with feedback from over 3 years of gene-silencing experiments, ensuring that the algorithm’s in-silico rules are guided and bolstered by real-world empirical evidence.
Why does Sigma list siRNA from several different NM sequences? Should I choose the #1 of each of the NM sequences listed, or should I choose numbers 1, 2, and 3 from one NM sequence?
When there is more than one NM sequence listed, this means that there are alternate transcripts for that particular gene. Our Rosetta Algorithm is run separately for each cDNA transcript.
In answer to your second question, you should choose 3 siRNAs from one RefSeq to ensure 3 unique target sequences.
How do I know which Predesigned siRNA I should I order? They are just numbered. What does this mean?
Sigma's Predesigned MISSION siRNA have been designed using a world-class siRNA design algorithm licensed from Rosetta Inpharmatics, a leader in advanced siRNA research. Critical rules incorporated into the best-in-class Rosetta siRNA design algorithm lead to siRNA of increased target specificity and knockdown for low abundance messages. The ranking for Predesigned siRNAs for our Rosetta Algorithm are from 1 to 10, 1 being the highest rank and 10 being the lowest. Positive control siRNAs or functionally Validated siRNAs are called out via the "siRNA Type column."