To utilize the information contained within a cell’s genes, the enzyme RNA polymerase must find the beginning of each gene (the promoter). Finding the beginning is a prodigious task: RNAP must start at a particular base pair of DNA, but the cell contains millions of base pairs to choose from. It has been proposed that gene-finding challenge is aided by a process termed ‘facilitated diffusion’ (FD). In FD, RNA polymerase first binds to a random position on DNA and then slides along the DNA like a bead on a string until it encounters the target DNA sequence.
In a recently published study in PNAS (1), biophysicists Larry Friedman and Jeffrey Mumm worked with Prof. Jeff Gelles in the Brandeis Biochemistry department to test key predictions of the FD model. They used a novel light microscope that Friedman and colleagues invented and built at Brandeis, a microscope that can directly observe the binding of an individual RNA polymerase to a single DNA. The scientists studied the σ54 RNA polymerase holoenzyme, an RNA polymerase found in most species of bacteria. Surprisingly, none of the three predictions of the FD model that the experiments tested were found to be valid, demonstrating that target finding by the polymerase is not accelerated by sliding along DNA. Friedman and colleagues instead propose that RNA polymerases are present in such large numbers that they can diffuse through the cell and efficiently bind to their target sites directly. The absence of FD may explain how other proteins can bind to positions on the DNA that flank gene start sites and yet not interfere with RNA polymerase finding the gene.
Is this the end of the story? Not likely, given previous publications suggesting FD plays a role for some other DNA binding proteins. Using single-molecule techniques like those developed in the Gelles lab, scientists in next few years should give us a better idea if FD is very rare or very common. [editor: as a chemical engineer, I'm sad to see FD not have a role -- it seemed like such a nice theory...]
Friedman LJ, Mumm JP, Gelles J. RNA polymerase approaches its promoter without long-range sliding along DNA. Proc Natl Acad Sci U S A. 2013 May 29. [Epub ahead of print]