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I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen.

It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409).

Is it a problem to use such a transposon, which contains the transposase within the IR regions?

I am concerned that because the transposase will always be expressed (since its coding sequence is carried around inside the transposon), the transposon will keep on "jumping".

How real is this problem from a practical point of view?

Thanks, J

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There are many natural transposons that are self propogating, hence your plasmid might be derived from one of those.

I can't be sure if it is a problem without knowing more details of the transposon or your experimental goals. However, it might be a good idea to make the transposon inducible, by replacing it's promoter with an inducible one such as pTet or pLacIq, along with including the cognate repressor.

A similar strategy is used in this paper, albeit not with transposons but other integrative and conjugative elements (ICEBs1) from Bacillus subtilis

Brophy, Jennifer AN, et al. "Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria." Nature microbiology 3.9 (2018): 1043-1053.

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