DSIR Assessing the Design of Highly Potent siRNA by Testing a Set of Cancer-Relevant Target Genes 英文参考文献.docVIP

DSIR:AssessingtheDesignofHighlyPotentsiRNAby TestingaSetofCancer-RelevantTargetGenes OdileFilhol1,2,3*,DelphineCiais1,2,3,ChristianLajaunie4,5,6,PeggyCharbonnier3,7,8,NicolasFoveau3,7,8 , Jean-PhilippeVert4,5,6,YvesVandenbrouck3,7,8 * 1CEA,DSV,iRTSV,LaboratoiredeBiologieduCanceretdel’Infection,Grenoble,France,2INSERMU1036,Grenoble,France,3Universite′ GrenobleI,Grenoble,France, 4MinesParisTech,CentreforComputationalBiology,Fontainebleau,France,5InstitutCurie,Paris,France,6INSERMU900,Paris,France,7CEA,DSV,iRTSV,Laboratoirede Biologiea` GrandeEchelle,Grenoble,France,8INSERMU1038,Grenoble,France Abstract Chemically synthesized small interfering RNA (siRNA) is a widespread molecular tool used to knock down genes in mammaliancells.However,designingpotentsiRNAremainschallenging.AmongtoolspredictingsiRNAefficacy,veryfew havebeenvalidatedonendogenoustargetsinrealisticexperimentalconditions.Wepreviouslydescribedatooltoassist 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 siRNAsequencesdesignedbyDSIRsilencedtheirtargetgenesbyatleast70%.Silencingefficacywassustainedevenwhen lowsiRNAconcentrationswereused.Thissystematicanalysisrevealedinparticularthat,forasubsetofgenes,theefficiency of siRNA constructs significantly increases when the sequence is located closer to the 59-end of the target gene coding sequence, suggesting the distance to the 59-end as a new feature for siRNA potency prediction. A new version of DSIR incorporating these newfindings, as wellas thelist of validatedsiRNA against thetestedcancer genes, has beenmade availableontheweb(http://biodev.extra.cea.fr/DSIR). Citation: Filhol O, Ciais D,LajaunieC, Charbonnier P, Foveau N, et al.(2012) DSIR: Assessing