Rather than the series of if { ... } elsif { ... } ... tests you could use a hash table to look up the base and use it as the fourth argument to substr to replace the original.

$ perl -Mstrict -Mwarnings -E '
my $dna        = q{AAGGTTCC};
my %compLU     = (
   A => q{T},
   T => q{U},
   G => q{C},
   C => q{G},
   );
my $complement = $dna;

for my $idx ( 0 .. length( $complement ) - 1 )
{
    substr $complement, $idx, 1, $compLU{ substr $complement, $idx, 1 
+};
}

say $dna;
say $complement;'
AAGGTTCC
TTCCUUGG
$
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I hope this is of interest.