my $a_ref = \'A';
my $c_ref = \'C';
my $t_ref = \'T';
# etc...
# Then storing these values in an array reference:
my $base_ref;
while ( <$fh> ) {
   # Get the correct values you need
   my $nuc_ref =   $base eq 'A' ? $a_ref
                 : $base eq 'C' ? $c_ref
                 : $base eq 'G' ? $g_ref
                 : $base eq 'T' ? $t_ref
                 : $n_ref;

   push @{$base_ref}, $nuc_ref;
}