Hi Archana, try like this,

use strict;
use warnings;

my $str ='"Transcription factor" promoter DNA "Transcription factor" p
+romoter DNA.';
my @str = split//, $str;
my $fla = 1;
for (@str){
    if (($_ eq "\"") && $fla)
    {
        $fla = 0;
    }elsif (($_ eq "\"") && !($fla)){
        $fla = 1;
    }
    $_ =~ s/ /\,/ if ($fla);
}

print join'',@str;
__END__
Output:
-------
"Transcription factor",promoter,DNA,"Transcription factor",promoter,DN
+A.
[download]

TIMTOWTDI, we can achieve the expected output using RegExp as of below:

$str =~ s/((?:(?!\").)*)(\"[^\"]+\")((?:(?!\").)*)/
my $fi = $1;my $se = $2; my $th = $3;
$fi =~ s| |\,|g;$th =~ s| |\,|g;
"$fi$se$th"/egs;
[download]