A study on the fundamental factors determining the efficacy of siRNAs with high C/G contents.
Although there are many reports about the efficacy of siRNAs, it is not clear whether those siRNAs with high C/G contents can be used to silence their target mRNAs efficiently. In this study, we investigated the structure and function of a group of siRNAs with high C/G contents. The results showed that single siRNAs against the Calpain, Otoferlin and Her2 mRNAs could induce different silencing effects on their targets, suggesting that the accessibility to target sequences influences the efficacy of siRNA. Unexpectedly, a single siRNA could target its cognate sequence in the 3'UTR of EEF1D or the 5'UTR of hTRF2 or CDC6. Their interaction induced different modes of gene silencing. Furthermore, the introduction of mutations into the 3' end of the passenger strand showed that the position and number of mutated nucleotides could exert some influence on the efficacy of siRNA. However, these mutations did not completely block the passenger strand from exerting its RNAi effect. Interestingly, our findings also indicated that the target mRNA might play essential roles in maintaining or discarding the guide strand in RISCs. Thus, the conclusion could be drawn that favorable siRNA sequences, accessible target structures and the fast cleavage mode are necessary and sufficient prerequisites for efficient RNAi.
Liao
Jie-Ying
JY
Systems Biology Research Center, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, PR China.
Yin
James Q
JQ
Chen
Fang
F
Liu
Tie-Gang
TG
Yue
Jia-Chang
JC
D001482:Base Composition; D001483:Base Sequence; D045744:Cell Line, Tumor; D004305:Dose-Response Relationship, Drug; D020868:Gene Silencing / Q000187:drug effects; D006801:Humans; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D012333:RNA, Messenger / Q000737:chemistry; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics / Q000494:pharmacology*
D012333:RNA, Messenger; D034741:RNA, Small Interfering