Integrated siRNA design based on surveying of features associated with high RNAi effectiveness

BMC Bioinformatics

Table 2 Non-redundant DRM rule set for the highest α level:RS_0.951.

Feature	F₁	F₂	F₅	F₆	F₇	F₈	F₁₃	F₁₄	F₁₅	F₁₆	F₁₇
Rule 1	√	√	√						√
Rule 2		√	√			√		√	√
Rule 3	√	√		√					√	√	√
Rule 4		√	√		√	√			√	√
Rule 5	√		√				√	√	√	√
Rule 6		√	√	√	√	√			√
Rule 7		√	√		√	√	√		√
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_m is 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) ≥ -22.72 KCal/Mol
F₁₇	Target site is on CDS

ISSN: 1471-2105