核苷酸
小干扰RNA
RNA干扰
配对
核糖核酸
碱基对
基因沉默
小RNA
反式siRNA
信使核糖核酸
化学
RNA沉默
生物
细胞生物学
分子生物学
遗传学
基因
物理
量子力学
超导电性
作者
Yoshito Kobayashi,Shen Tian,Kumiko Ui-Tei
出处
期刊:Genes
[MDPI AG]
日期:2022-02-09
卷期号:13 (2): 319-319
被引量:6
标识
DOI:10.3390/genes13020319
摘要
In RNA interference (RNAi), small interfering RNA (siRNA) suppresses the expression of its target mRNA with a perfect complementary sequence. In addition, siRNA also suppresses the expression of unintended mRNAs with partially complementary sequences mainly within the siRNA seed region (nucleotides 2-8). This mechanism is highly similar to microRNA (miRNA)-mediated RNA silencing, and known as the siRNA-mediated off-target effect. Previously, we revealed that the off-target effect is induced through stable base-pairing between the siRNA seed region and off-target mRNAs, but not induced through unstable base-pairing. However, in our recent study, we found that the siRNA seed region consists of two functionally different domains: nucleotides 2-5, essential for off-target effects, and nucleotides 6-8, involved in both RNAi and off-target effects. In this study, we investigated the most responsible region for the off-target effect by conducting a comprehensive analysis of the thermodynamic properties of all possible siRNA subregions that involved a machine learning technique using a random sampling procedure. As a result, the thermodynamic stability of nucleotides 2-5 showed the highest positive correlation with the off-target effect, and nucleotides 8-14 showed the most negative correlation. Thus, it is revealed that the siRNA off-target effect is determined by the base-pairing stabilities of two different subregions with opposite effects.
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