If A -> B and later that B-> T so what will be if we have some B's in our dna ?
These B's will be replace too so it's not good option in my opinion.

looks very nice but that's 6 runs through the string...

as for me one of the best solution!!!

This solution is too slow anyway (if we are talking about performance) to bother about such minor optimization at all.

not really, i have almost similar benchmarks

Use of char constants instead of String constants will make this solution faster.