siRNA target selection problem
Posted 20 January 2003 - 03:23 AM
thanks in advance for you responses
Posted 20 October 2004 - 06:00 PM
Posted 16 November 2004 - 07:51 PM
If anyone can suggest good papers for designing that would be great.
Posted 16 November 2004 - 10:49 PM
Here are some resources on the web:
The original Tuschl's rules:
Rational siRNA design paper:
This nice Excel macro implements the algorithms reported in the above paper. I have used it for designing all my siRNAs. I recommend it.
Edited by pcrman, 16 November 2004 - 10:50 PM.
Posted 17 November 2004 - 08:37 PM
Can I just clarify - once you have used the Excel program you blast the DNA sequences, then any good candidates you use the RNA seq to order siRNA? Do you add the Tuschl TT? (if so where/why - I've never quite got my head around this).
Also, how many synthetic siRNA do you normally begin with to check function?
Posted 17 November 2004 - 09:57 PM
The excel program gives a list of targets and corresponding siRNAs ranked by total score. the siRNAs are 19 nt. First, you have to do a blast [using not just the 19 bp but incluing some more bps both upstream and downstream because UCSC Blat program (my favorite) won't accept queries that are too short]. If there is no obvious homology with other non target sequence, I will pick up those with high scores. At this time you can take Tuschl's rule into consideration such the target should be xx bp downstream of the ATG and ect. After you find a desired target, usually you just copy the siRNA sequence (19 nt) into the vendor's order form, if you choose add dTT to the 3 overhang, they will be added automatically.
target: 5' - CTA GAC GGT ACG TGA TTA G siRNA sense: 5' - CUA GAC GGU ACG UGA UUA G [dT][dT] antisense: 5' - C UAA UCA CGU ACC GUC UAG [dT][dT]Here you can find an illustrated explanation.
Edited by pcrman, 17 November 2004 - 09:59 PM.
Posted 19 November 2004 - 09:06 AM
is also implemented in the following program (SVM RNAi):
You would need to download the stand-alone version, which is currently 3.6. The demo is fully functional.