[EMBOSS] siRNA improvements
Gary Williams, Tel 01223 494522
gwilliam at hgmp.mrc.ac.uk
Wed Dec 3 09:49:06 UTC 2003
Thanks for the suggestions.
I'll take a look.
Stefanie Lager wrote:
> 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.
> http://fastmail.ca/ - Fast Secure Web Email for Canadians
Gary Williams MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500 Fax: +44 1223 494512
E-mail: name at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk
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