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siRNA design: where it should be targeted?


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#1 akim

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Posted 25 February 2005 - 04:52 PM

I am new to siRNA world. I need to know where I should design siRNA against, that is, 5'UTR, ORF, or 3'UTR. Is there any advantage or disadvantage amongst?
According to an editorial article (Nature Cell Biology 2003, Vol.5: 489-490), siRNA targeted against 3'UTR will not have a translational effects often associated with miRNA (see p490, section under '4. Functional controls').
I am not sure how siRNA trageted aganist 3'UTR will knock out the traget gene. After cleavage, is there not a mRNA piece containing pettty much complete mRNA sequence since it was cleaved at 3'UTR?
Can any one enlighten me on this?
Thanks for sharing your brain power in advance.

#2 fred_33

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Posted 26 February 2005 - 06:54 AM

hi
according to the fact that in the cell there is more mRNA than native RNA, it's better to chose a sequence inside the mRNA. You're right, it seems that choosing a sequence in the 3' UTR is less effective than in other parts.
Elbashir and al. have observed that siRNA that start by AA are more effective (in
S Elbashir et al. Functional anatomy of siRNA for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 2001

in order to analyse general features for working siRNA, you can see siRNA databases (like the ambion's one).
Moreover they have sumed up guidelines for design of siRNA.
You can see these at http://www.ambion.co.../tb/tb_506.html

Fred

#3 expresson_help

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Posted 28 February 2005 - 07:50 AM

Our research shows that as long as the region is accessible and isn't buried in secondary structure it doesn't matter, although we do notice that the 3' UTR is often less accessible than the 5'UTR and coding region.

#4 akim

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Posted 28 February 2005 - 10:25 AM

Thanks for the inputs!
I have also been considering 2nd structure of mRNA, and am going to use 'em as a guidline when I pick one from the suggested siRNA list by various programs.
This site is so cool!
Cheers!!!!!

#5 expresson_help

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Posted 01 March 2005 - 03:17 AM

how exactly are you going to take secondary structure into account? This cannot be done accurately by computer algorithms.




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