  Recently the physical characterization of a number of biological processes
has proven indispensable for a full understanding of natural phenomena. One
such example is the mechanical properties of transcription, which have been
shown to have significant effects in gene expression. In this letter we
introduce a simple description of the basic physical elements of transcription
where RNA elongation, RNA polymerase rotation and DNA supercoiling are coupled.
The resulting framework describes the relative amount of RNA polymerase
rotation and DNA supercoiling that occurs during RNA elongation. Asymptotic
behavior is derived and can be used to experimentally extract unknown
mechanical parameters of transcription. Incorporation of mechanical limits to
RNA polymerase is accomplished yielding an equation of motion for DNA
supercoiling and RNA elongation with transcriptional stalling. Important
implications for gene expression, chromatin structure and genome organization
are discussed.
