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E-RNAi uses primer3 for the design of primer pairs required to amplify templates for long dsRNAs by PCR. Several primer design parameters can be adjusted by the user, such as melting temperature, GC content, primer pair penalty and desired amplicon length. These settings are applied to all RNAi reagents designed in a single run, which facilitates efficient (high-throughput) PCR of all templates. It is recommended to use the same primer design settings for all reagents that are going to be synthesized side by side.

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