dsir assessing the design of highly potent sirna by testing a set of cancer-relevant target genesdsir评估设计的高度有效的核测试一组癌症相关目标基因.pdfVIP

DSIR: Assessing the Design of Highly Potent siRNA by Testing a Set of Cancer-Relevant Target Genes Odile Filhol1,2,3*, Delphine Ciais1,2,3, Christian Lajaunie4,5,6, Peggy Charbonnier3,7,8, Nicolas Foveau3,7,8, Jean-Philippe Vert4,5,6, Yves Vandenbrouck3,7,8* ´ 1 CEA, DSV, iRTSV, Laboratoire de Biologie du Cancer et de l’Infection, Grenoble, France, 2 INSERM U1036, Grenoble, France, 3 Universite Grenoble I, Grenoble, France, 4 Mines ParisTech, Centre for Computational Biology, Fontainebleau, France, 5 Institut Curie, Paris, France, 6 INSERM U900, Paris, France, 7 CEA, DSV, iRTSV, Laboratoire de ` Biologie a Grande Echelle, Grenoble, France, 8 INSERM U1038, Grenoble, France Abstract Chemically synthesized small interfering RNA (siRNA) is a widespread molecular tool used to knock down genes in mammalian cells. However, designing potent siRNA remains challenging. Among tools predicting siRNA efficacy, very few have been validated on endogenous targets in realistic experimental conditions. We previously described a tool to assist efficient siRNA design (DSIR, Designer of siRNA), which focuses on intrinsic features of the siRNA sequence. Here, we evaluated DSIR’s performance by systematically investigating the potency of the siRNA it designs to target ten cancer- related genes. mRNA knockdown was measured by quantitative RT-PCR in cell-based assays, revealing that over 60% of siRNA sequences designed by DSIR silenced their target genes by at least 70%. Silencing efficacy was sustained even when low siRNA concentrations were used. This systematic analysis revealed in particular that, for a subset of genes, the efficiency of siRNA constructs significantly increases when the sequ