siRNA design: where it should be targeted? - (Feb/25/2005 )

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.

-akim-

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.com/techlib/tb/tb_506.html

Fred

-fred_33-

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.

-expresson_help-

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!!!!!

-akim-

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

-expresson_help-

QUOTE (akim @ Feb 28 2005, 09:25 PM)

Hi akim

If you are looking to add mRNA 2nd structure check this 2 papers on
JMB www.sciencedirect.com

Local RNA Target Structure Influences siRNA Efficacy: Systematic Analysis of Intentionally Designed Binding Regions
Journal of Molecular Biology, In Press, Corrected Proof, Available online 1 April 2005,
Steffen Schubert, Arnold Grünweller, Volker A. Erdmann and Jens Kurreck

Local RNA Target Structure Influences siRNA Efficacy: A Systematic Global Analysis
Journal of Molecular Biology, In Press, Uncorrected Proof, Available online 22 March 2005,
Marita Overhoff, Martina Alken, Rosel Kretschmer-Kazemi Far, Marc Lemaitre, Bernard Lebleu, Georg Sczakiel and Ian Robbins

-hakim-