MCLAB :: Tool :: Sirna design

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

T_mis between 20 and 60°C

F₁₄

Binding energy of N16–N19 > -9 KCal/Mol

F₁₅

Binding energy of N16–N19 – binding energy of N1–N4 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.