use strict;
use warnings;

while ( <DATA> ) {
   s/([^,])"(?!,|$)/$1""/g;
   print $_;
}

__DATA__
"A","B"",""C","D","E"
""F",
,"G""
"HI"J"K"L","M"
1,2,3,"t"l"r",4,5,6