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The XY pairs are not replicated. To replicate them would require the presence of a slew of specialized proteins that can deal with XY pairs.

The achievement is that the E. Coli lifetime is not affected. The XY's are probably inserted in a part of the DNA that is not transcribed.

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The paper specifically states that these unnatural base pairs were chosen because they can be handled by natural polymerases. Also, the only way to maintain a plasmid over time is to replicate it. In fact, the whole logic of the strategy is to have Cas9 target mutations to the plasmid so that loss of the XY base pair during replication would lead to loss of the plasmid, and thus loss of the antibiotic resistance gene that it also carried.

I 150% guarantee you they are in a place that is transcribed. Otherwise there would be no selection pressure to maintain it and the bacteria would kick it out in favor of one of the plain old bases.

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