No need for the square brackets: 
$dna = "NNNNATCGNNNTCGANNN";
$dna =~ s/^N+//;
$dna =~ s/N+$//;
print "$dna\n"
__END__
ATCGNNNTCGA

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In reply to Re^2: Removing Flanking "N"s in a DNA String by ikegami
in thread Removing Flanking "N"s in a DNA String by monkfan

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