2000/09/13 by Kevin J. Harrington, K. J. Harrington, R. B. Laughlin +1
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Diffusion and Search Dynamics #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #cond-mat.soft #physics.bio-ph #q-bio
paper · pdf · doi:10.1073/pnas.240431598
8 pages of RevTeX, 2 eps figures
arxiv created 2000/09/13 · openalex publication_date 2001/04/17 · arxiv updated 2009/11/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255, 809-812 and von Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244, 36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.