My first bioperl:

perl -MMath::Permute::List -e "permute {print qq(@_\n)}  qw(A A T T G G C C);"

Best regards, Karl

Update: I don't know if that is what you need because i'm no biologist :-(

P.S.: Change ticks to ' if not on windoz.

Update 2: Perhaps i missed something essential in your specs:

"...the composition of elements in the DNA string remain the same"

What does that mean?

And the missing link: Math::Permute::List.