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. 2008 Apr 10;13(2):283–302. doi: 10.2478/s11658-008-0001-1

A study on the fundamental factors determining the efficacy of siRNAs with high C/G contents

Jie-Ying Liao 1, James Q Yin 1,✉, Fang Chen 1, Tie-Gang Liu 2, Jia-Chang Yue 1
PMCID: PMC6275720  PMID: 18197393

Abstract

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.

Keywords: siRNA, RNAi, mRNA, Local structure, Gene silencing

Full Text

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Abbreviations

Ago

argonaute

C

cytosine

Calp

calpain

ds

double-strand

G

guanine

Her2

v-erb-b2 erythroblastic leukemia viral oncogene homolog 2

HRP

peroxidase

Otof

otoferin

RISC

RNA-induced silencing complex

RNAi

RNA interference

RNase

ribonuclease

siRNA

short interfering RNA

TMB

3,3′,5,5′ tetramethylbenzidine

Contributor Information

James Q. Yin, Phone: 86-010-64888572, FAX: 86-010-64888572, Email: jqwyin@sun5.ibp.ac.cn

Jia-Chang Yue, Email: yuejc@sun5.ibp.ac.cn.

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