Sirna design
Sirna design

GenScript siRNA Target Finder.

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GenScript siRNA Target Finder.

The availability of the large and diverse siRNA dataset from siRecords  have allowed the development of highly effective and generally applicable siRNA design rule sets. Together with ever improving RNAi lab techniques, these design rule sets are expected to make siRNAs a more useful tool for molecular genetics, functional genomics, and drug discovery studies.

List of features:

Feature Index Feature Names

F1 2nd nucleotide = A
F2 4th nucleotide = C
F3 6th nucleotide <> C
F4 7th nucleotide <> U
F5 9th nucleotide = C
F6 17th nucleotide = A
F7 18th nucleotide <> C
F8 19th nucleotide = (A/U)
F9 At least three (A/U)s in the seven nucleotides at the 3' end
F10 No occurrences of four or more identical nucleotides in a row
F11 No occurrences of G/C stretches of length 7 or longer
F12 G/C content is between 35 and 60%
F13 Tm is between 20 and 60°C
F14 Binding energy of N16N19 > -9 KCal/Mol
F15 Binding energy of N16N19 binding energy of N1N4 is between 0 and 1 KCal/Mol
F16 Local folding potential (mean) e -22.72 KCal/Mol
F17 Target site is on CDS

Reference: Wuming Gong , Yongliang Ren , Qiqi Xu , Yejun Wang , Dong Lin , Haiyan Zhou and Tongbin Li Integrated siRNA design based on surveying of features associated with high RNAi effectiveness Bioinformatics. , BMC Bioinformatics 2006, 7:516.
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