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Yea I read that entire paper! The main issue seems to be 1: The polymerases don't replicate the unnatural ones well 2: They have only tested it in a single locus 3: The transport proteins make the cells sickly 4: You have to buy purified nucleotides to give to the cells. In all, pretty expensive. I actually have already designed a CRISPR system (I was bored so I planned all primers/synthesis needed) that can force the cell to faithfully replicate the Xs. If the cell mutates the X, any combination will cause the cell to kill itself.
But really, this is exciting research! With another base pair, you could hypothetically make tRNA codons with 2 base pairs instead of 3 and still include all of the genetic code... A "decompression" mechanism if you will. I'd love to be a part of this research later, but right now its not mature enough. Once they make enzymes that create the unnatural nucleotides in the cell, I want to hop on this research boat and apply it to what I am currently doing.