use strict;
use warnings;

my $str ='"Transcription factor" promoter DNA "Transcription factor" promoter 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,DNA.