[EMBOSS] siRNA improvements

Stefanie Lager stefanielager at fastmail.ca
Wed Dec 3 07:17:18 UTC 2003


It would be nice if the EMBOSS application sirna could incorporate
simple calculation of free energy, to improve the siRNA design. Lately
several reports on siRNA design (reviewed in Silva et al 2003) have
showed the importance of making the 5' end of the antisense strand
less stable than the 3' end (Schwarz et al 2003). Also the center part
should show a lower internal stability (Khvorova et al 2003). Simple
energy profiles can be calculated by the method of Mathews et al
(Mathews et al 1999). Several of the commercial siRNA design servers
have already incorporated free energy parameters in the design, and it
would really be nice to have an alternative.


Silva JM, Sachidanandam R, Hannon GJ.
Free energy lights the path toward more effective RNAi  
Nat. Genet. 2003, 35:303-305.

Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. 
Asymmetry in the assembly of the RNAi enzyme complex.
Cell. 2003 115:199-208.

Khvorova A, Reynolds A, Jayasena SD. 
Functional siRNAs and miRNAs exhibit strand bias.
Cell. 2003 115:209-216.

Mathews DH, Sabina J, Zuker M, Turner DH. 
Expanded sequence dependence of thermodynamic parameters improves
prediction of RNA secondary structure.
J Mol Biol. 1999 288:911-940.

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