Already biology itself has modified it's DNA bases to identify self and not-self, silenced and active. RNA bases in tRNA are, what, 30% modified minimum? with a huge variety of mods. And that's partly to allow for non-Watson Crick recognition in the tRNA core fold.
So, er, the point is that modified bases already exist and I could totally see evolution just encoding them into tri-phosphates and allowing recognition by polymerases. I could also see interesting unethical lab accidents in which eeeeeeevil scientists somehow incorporate the plethora of modified bases (anything from ratioactive tags to variations on ATCG), available to lab scientists, but that's just me.
You are also totally correct that all the filler, no transcribed stuff could be removed, and with the more efficient use of space you'd have DNA a lot more like mitochondrial DNA, with little extra stuff, but you'd probably have less control over silencing and regulation, and if you really go all mitochondrial on it, you might relax specificity on the wobble base recognition and you'd have reeeeeeally interesting increase mutational rates. Possibly just shortened lifespan stuff, possibly all X-men, but let us not speak of the X-men froonium genetics.
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So, er, the point is that modified bases already exist and I could totally see evolution just encoding them into tri-phosphates and allowing recognition by polymerases. I could also see interesting unethical lab accidents in which eeeeeeevil scientists somehow incorporate the plethora of modified bases (anything from ratioactive tags to variations on ATCG), available to lab scientists, but that's just me.
You are also totally correct that all the filler, no transcribed stuff could be removed, and with the more efficient use of space you'd have DNA a lot more like mitochondrial DNA, with little extra stuff, but you'd probably have less control over silencing and regulation, and if you really go all mitochondrial on it, you might relax specificity on the wobble base recognition and you'd have reeeeeeally interesting increase mutational rates. Possibly just shortened lifespan stuff, possibly all X-men, but let us not speak of the X-men froonium genetics.
...I'll stop now.