发信人: cDNA (运动狂魔之岁月蹉跎), 信区: Biology
标 题: Re: HELP: how to select RNAi target sequence
发信站: Unknown Space - 未名空间 (Sun Jan 4 02:35:11 2004), 站内信件

This issue is exactly one of my research projects. So just give my 2
cent.

1.the efficacy of siRNA vary dramatically against the same target gene.
By far, there is NO clear rule of selection.

2.ALL software can achieve no more than 70% of accuracy of prediction,
no matter where you find it or whatever they claim themselves could
achieve.

3.There probably endless factors which could affect the efficacy of
siRNA. The real efficacy is combination of all, though some factors do
contribute more others. Some those important factors are:

A.Accessibility: RNA secondary structure, RNA binding protein,
chaperon protein.. so, basically, m-fold or m-fold based software can
tell you nothing about the accessibility.
B.Thermal stability: only one strand of siRNA will bind to RISC, and
the selection is almost target independent. if the thermal stability
of 5' end of antisense strand is less stable than the 3' end, RISC
will prefer to selected the antisense strand, leading to increasing
the number of functional RISC.
C. GC content, position of target region ( 5'end / 3' end
/CDS/5UTR/3UTR) have much less effect compare to accessibility and
thermal stability of the end.
D.Which factor is more important is case by case.


【 在 smallstone (小丸子) 的大作中提到: 】
: Does it matter which region you target, i.e. c-terminal or N-terminal or UTR?
: And does GC content affect the result?


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