Functional Genomics & RNAi

Design Site FAQ


TargeTron® Gene Knockout System FAQs
Adapting TargeTron® to Other Organisms FAQs


TargeTron® Design Site FAQs

 

  1. It is recommended to check my sequence of interest for insertion sites on the TargeTron Test Site before purchasing a kit. Why?
    The test site will help you determine the number of potential insertion sites in your sequence of interest. This is especially important for small DNA sequences (400bp or less) as smaller sequences may not have potential insertion sites. The locations of the insertion sites and the primer designs for those insertion sites are only available upon purchase of the kit.

  2. Is the cost of the primers included in the price of the TargeTron kit?
    No, the primers must be purchased separately. Primers can be easily purchased through the website by using the link to Sigma-Genosys at the bottom of the TargeTron Design Site output page.

  3. When designing my primers to mutate the intron using the TargeTron Design Site, the site suggests choosing the primer sets with the higher S-values and the lower E-values. What does this mean?
    DNA target sequences were scored (S-value) using a log-odds score, which measures whether the probability that the sequence generated by the model is greater than the probability that the sequence was generated by chance (null model). A positive score means that the model fits the group II intron target sequence better than chance (null model). Therefore, the higher the score (S-value), the better the chance that the target site is "real" and that the intron will insert efficiently. (Perutka et. al. 2003. Use of Computer-designed Group II Introns to Disrupt Escherichia Coli DexH/D-box Protein and DNA Helicase Genes. J. Mol. Bio. 336, 421-429).
    The E-value estimates the expected number of false positives at or above the score (S-value).


  4. Can I save the primer sequences generated by the TargeTron Design Site?
    Yes. There is a link to download the primer sequences to a text file for future reference or to order primers. Downloading your results is important. Once you leave the TargeTron Design Site, you will not be able to access the primer sequences again without using another access.
    Look for the text below and the link to download results to a text file.

Below are the potential insertion sites and the primer sets corresponding to the design options. Please download the results for reference and/or to order primers. Once this window is closed, the results cannot be viewed without using an additional access.

Download results to a text file.



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TargeTron® Gene Knockout System