Kinetic versus energetic discrimination in biological copying

Phys Rev Lett. 2013 May 3;110(18):188101. doi: 10.1103/PhysRevLett.110.188101. Epub 2013 May 1.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism*
  • Kinetics
  • Models, Biological*
  • Stochastic Processes
  • Thermodynamics

Substances

  • DNA-Directed DNA Polymerase