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The gene silencing effect of short interfering RNA (siRNA) is known to varystrongly with the targeted position of the mRNA. A number of hypotheses havebeen suggested to explain this phenomenon. We would like to test if thispositional effect is mainly due to the secondary structure of the mRNA at thetarget site. We proposed that this structural factor can be characterized by asingle parameter called "the hydrogen bond (H-b) index", which represents theaverage number of hydrogen bonds formed between nucleotides in the targetregion and the rest of the mRNA. This index can be determined using acomputational approach. We tested the correlation between the H-b index and thegene-silencing effects on three genes (Bcl-2, hTF and cyclin B1) using avariety of siRNAs. We found that the gene-silencing effect is inverselydependent on the H-b index, indicating that the local mRNA structure at thetargeted site is the main cause of the positional effect. Based on thisfinding, we suggest that the H-b index can be a useful guideline for futuresiRNA design.

Using a hydrogen-bond index to predict the gene-silencing efficiency of siRNA based on the local structure of mRNA