I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. Transcription creates positive supercoils ahead of the RNA polymerase and negative supercoils behind it, and according to my TA's, this causes enough mechanical strain to sometimes even stop transcription from occurring. Why doesn't the polymerase just rotate around the DNA to relieve the strain?
The video below is helpful to communicate what the question is asking. The model I was taught is that the polymerase proceeds on a linear path, not a helical path, and thus the transcription bubble forces positive supercoils ahead and negative behind. The video shows this with a pen in place of the polymerase and a shoelace in place of the DNA; displacement of the pen tightens coils downstream and loosens them upstream. The way this seems to depart from reality is the desk or backdrop in the video, which keeps the pen from spinning, and the air, which offers no friction or thermal energy. In real life, the polymerase isn't a pen and the DNA isn't sitting on a desk and the surrounding medium is aqueous and of course the whole thing is at a smaller physical scale such that heat is experienced differently. But why doesn't the pen (polymerase) just spin?
P.S. I also looked at Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?, but I'm not sure what to take from that thread. Some answers disagree and others only mention unwinding, which afaik is a much lesser source of strain compared to the lack of rotation.