title: Kinetic versus energetic discrimination in biological copying.
abstract: We study stochastic copying schemes in which discrimination between a right and a wrong match is achieved via different kinetic barriers or different binding energies of the two matches. We demonstrate that, in single-step reactions, the two discrimination mechanisms are strictly alternative and cannot be mixed to further reduce the error fraction. Close to the lowest error limit, kinetic discrimination results in a diverging copying velocity and dissipation per copied bit. On the other hand, energetic discrimination reaches its lowest error limit in an adiabatic regime where dissipation and velocity vanish. By analyzing experimentally measured kinetic rates of two DNA polymerases, T7 and Polγ, we argue that one of them operates in the kinetic and the other in the energetic regime. Finally, we show how the two mechanisms can be combined in copying schemes implementing error correction through a proofreading pathway.
authors.affiliation: Max Planck Institute for the Physics of Complex Systems, Noethnitzer Strasse 38, 01187 Dresden, Germany.
authors.forename: Pablo
authors.initials: P
authors.lastname: Sartori
authors.forename: Simone
authors.initials: S
authors.lastname: Pigolotti
mesh_terms: D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008954:Models, Biological; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D004259:DNA-Directed DNA Polymerase