The following video clip shows a model of how RNA polymerase could read a double-stranded helical template (often negatively supercoiled) without the nascent RNA becoming irremediably entangled around the DNA. Recall that the displacement of the transcription bubble along the template requires rotation of the bubble around the template axis.
The original "Quicktime" movie was prepared by Nello Bossi. Rob Edwards created two animated gif images from the original. The faster image has a frame delay of 0.1 secs and is essentially the same as the movie, and the slower image has a frame delay of 0.5 secs. Both should be displayed in your browser.
The model proposes that binding of RNA polymerase to the promoter and formation of the transcription bubble "inoculates" the formation of a plectonemic supercoiled branch that extrudes as transcription goes on. Maintenance of an apical position by RNA polymerase prevents RNA/DNA entanglement. The movie is largely inspired by the electron micrographs of Heggeler-Bordier et al. (1992) EMBO J. 11: 667-672. In the animated sequence, the template is a small negatively supercoiled circular DNA molecule. The transcribed region spans roughly one-fourth of the circle.
This animation and the accompanying explanation was produced by:
Dr. Lionello Bossi
Centre de Genetique Moleculaire CNRS
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Last modified September 23, 2004