2007
DOI: 10.1093/nar/gkm088
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Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

Abstract: Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver operating characteristics (ROC) and correlation analyses, the best programs were BioPredsi, ThermoComposition and DSIR. We also studied individual parameters that significantly and consistently co… Show more

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Cited by 139 publications
(149 citation statements)
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“…To knock down endogenous BC200 RNA, we designed 4 siRNAs to target BC200 RNA in accordance with Matveeva et al 24 for maximum silencing efficiency with low off-target effects and tested for their gene silencing effects. Among them siBC200 I and siRNA200 II were most effective ones.…”
Section: Depletion Of Bc200 Rna Disrupts the Migration And Invasion Omentioning
confidence: 99%
“…To knock down endogenous BC200 RNA, we designed 4 siRNAs to target BC200 RNA in accordance with Matveeva et al 24 for maximum silencing efficiency with low off-target effects and tested for their gene silencing effects. Among them siBC200 I and siRNA200 II were most effective ones.…”
Section: Depletion Of Bc200 Rna Disrupts the Migration And Invasion Omentioning
confidence: 99%
“…There are several algorithms to select siRNAs of highperformance [182,183,184,185,186], however it is impossible to predict precisely silencing activity of any particular siRNA in vivo. In addition, the design of siRNA targeting chimeric or mutant genes represent of complex task since the limitations of target site selection does not allow to use these algorithms for choosing the sequence siRNA.…”
Section: Resultsmentioning
confidence: 99%
“…This is illustrated in Figure 1. software's are available to design of effective siRNA targeting specific genes [13][14][15][16]. Then these exogenous siRNA are synthesized by chemical synthesis, in vitro transcription or transfection of plasmid/viral vectors containing siRNA sequences for expression in cells [17][18][19].…”
Section: Mechanism Of Rna Interferencementioning
confidence: 99%