This method reads the DNA file a line at a time in an infinite while loop, accumulating the lines in a buffer until the buffer doesn't end with an 'n'. Then a global replace of any first and last 'n's is done and the modified buffer is then printed to the output file and cleared. When the script detects that end-of-file has been found, it modifies and prints the buffer before exiting the infinite loop and closing the filehandles.

use strict;
use warnings;

open my $dnaFH, q{<}, \ <<'EOD' or die qq{open: HEREDOC: $!\n};
acacccacacacaccacacccacacaccacacccacacccacacaccaca
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaacccnnnnnnnnnnnnnnnnnnnnnnnnnnnccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
ggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnaccctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
gaccctgannnnnnncccccgaccccnnnnnnngccctaaccctaaccct
gaccctgannnnnnnnnnnnnnctaacccgaacccgaacccgaaccnnnn
EOD

my $rxReplaceN = qr
   {(?xi)
       (?<![nN\n])n
       |
       n(?![nN\n])
       |
       n(?=\n[^nN])
       |
       n(?=\n\z)
   };

my $outFile = q{spw697207.out};
open my $outFH, q{>}, $outFile
   or die qq{open: > $outFile: $!\n};

my $acc = q{};

while ( 1 )
{
    emitAcc(), last if eof $dnaFH;
    $acc .= <$dnaFH>;
    emitAcc() unless $acc =~ m{[nN]$};
}

close $dnaFH or die qq{close: HEREDOC: $!\n};
close $outFH or die qq{close: > $outFile: $!\n};

sub emitAcc
{
    $acc =~ s{$rxReplaceN}{^}g;
    print $outFH $acc;
    $acc = q{};
}
[download]

The output.

acacccacacacaccacacccacacaccacacccacacccacacaccaca
^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn^
cccacaccacacccacacaccacacaccacacccacacccacacacacca
cacccacacaccacacccacacacaccctaaccctaacccctaaccccta
accctaaccc^nnnnnnnnnnnnnnnnnnnnnnnnn^ccctaaccctaac
ccctaaccctaaccctaaccgtaaccctaaccctttaccctaacccgaac
ccctaac^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn^ggggg
gaccctgaccgtgaccctgaccctaacccgaacccgaacccgaaccccga
accccgaaccccgaaccccaaccccaaccccaaccccaaccctaacccct
caccctcaccctcgacccccgacccccgacccccgacccccaccccgaac
gg^nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnn^accctaaccctaaaaccctaaccctagcc
ctagccctagccctagccctaacccctaacccctaaccctaagccgaagc
gaccctga^nnnnn^cccccgacccc^nnnnn^gccctaaccctaaccct
gaccctga^nnnnnnnnnnnn^ctaacccgaacccgaacccgaacc^nn^
[download]

I hope this is of interest.

Cheers,

JohnGG