Structure-Based Design of Novel Chemical Modification of the 3鈥?Overhang for Optimization of Short Interfering RNA Performance

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• 作者：Lexing Xu ; Xin Wang ; Hongwei He ; Jinming Zhou ; Xiaoyu Li ; Hongtao Ma ; Zelin Li ; Yi Zeng ; Rongguang Shao ; Shan Cen ; Yucheng Wang
• 刊名：Biochemistry
• 出版年：2015
• 出版时间：February 10, 2015
• 年：2015
• 卷：54
• 期：5
• 页码：1268-1277
• 全文大小：551K
• ISSN：1520-4995

文摘

Short interfering RNAs (siRNAs) are broadly used to manipulate gene expression in mammalian cells. Although chemical modification is useful for increasing the potency of siRNAs in vivo, rational optimization of siRNA performance through chemical modification is still a challenge. In this work, we designed and synthesized a set of siRNAs containing modified two-nucleotide 3鈥?overhangs with the aim of strengthening the interaction between the 3鈥?end of the siRNA strand and the PAZ domain of Ago2. Their efficiency of binding to the PAZ domain was calculated using a computer modeling program, followed by measurement of RNA鈥揂go2 interaction in a surface plasmon resonance biochemical assay. The results suggest that increasing the level of binding of the 3鈥?end of the guiding strand with the PAZ domain, and/or reducing the level of binding of the sense strand through modifying the two-nucleotide 3鈥?overhangs, affects preferential strand selection and improves siRNA activity, while we cannot exclude the possibility that the modifications at the 3鈥?end of the sense strand may also affect the recognition of the 5鈥?end of the guiding strand by the MID domain. Taken together, our work presents a strategy for optimizing siRNA performance through asymmetric chemical modification of 3鈥?overhangs and also helps to develop the computer modeling method for rational siRNA design.