IIUC your question, which I'm not completely sure about, and taking into account Skeeve's comment, I'm giving you a (hopefully correct) hint/incomplete solution:
my $allow=join '|', qw/AA AG GC GT CA CG TT TC/;
my $disallow=join '|', qw/AC AT GG GA CC CT TG TA/;
# ...
my @chunks=/(?:$allow).*?(?=$disallow)/g;