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I heard I should use a scrambled control that has the same GC content as my siRNA. Isn't that better than a random sequence?

A true scrambled control containing the same base composition as your target specific siRNA might be considered a good non-specific control, provided that the scrambled siRNA has been verified to not inadvertently target another gene. However, experimental data indicate that even when no known target is identified, certain non-targeting siRNAs result in some cellular toxicity. With respect to preserving the overall base content (or GC content), Dharmacon scientists have found that this is less critical as the relative position of the bases will also have an impact on interactions with the silencing machinery. Until a better method is available for predicting the potential for toxicity or non-specific effects, it is recommended that a non-targeting siRNA that has been validated and determined to be non-functional or inert be used as a negative control. download our Technical Note: Effective Controls for RNAi Experiments to learn more.