Copying information is a fundamental task of biological systems that has to be performed at a finite temperature. There is agreement that this fact alone implies a lower limit on the error rate. However, contrasting results have been obtained regarding how this limit is approached. For instance, it is not clear when it can be achieved in a slow, quasi-adiabiatic regime or in a fast and highly dissipative one. In this paper, by means of analytical calculations and numerical simulations, we unravel a common feature of stochastic copying systems: the existence of two radically different copying modes. The first is based on different kinetic barriers , and is characterized by a high speed and high dissipation close to the lowest possible error. The second is based on energy differences between right and wrong copies, and is characterized by the fact that minimum copying error can be achieved at low speed and low dissipation. In models characterized by a single copying step, we demonstrate thatthese modes are alternative, i.e. they cannot be mixed to further reduce the minimum error . However, the two modes can be combined in multi-step reactions, such as in models implementing error correction through a proofreading pathway. By analyzing experimentally measured kinetic rates of two seemingly similar DNA polymerases, T7 and Pol\gamma, we argue that one of them operates in the kinetic and the other in the energetic regime  .
We study stochastic copying schemes in which discrimination between a right and a wrong match is achieved via different kinetic barriers or different binding energy of the two matches. We demonstrate that, in single-step reactions, the two discrimination mechanisms are strictly alternative and can not 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 opposite, 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 Pol\gamma, 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 .
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Copying information is a fundamental task of biological systems that has to be performed at a finite temperature. There is agreement that this fact alone implies a lower limit on the error rate. However, contrasting results have been obtained regarding how this limit is approached. For instance, it is not clear when it can be achieved in
We study stochastic copying schemes in which discrimination between a right and
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slow, quasi-adiabiatic regime or in a fast and highly dissipative one. In this paper, by means of analytical calculations and numerical simulations, we unravel a common feature of stochastic copying systems: the existence of two radically different copying modes. The first is based on
wrong match is achieved via
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, and is characterized by a high speed and high dissipation close to the lowest possible error. The second is based on energy differences between right and wrong copies, and is characterized by the fact that minimum copying error can be achieved at low speed and low dissipation. In models characterized by a single copying step, we demonstrate thatthese modes are alternative, i.e. they cannot
or different binding energy of the two matches. We demonstrate that, in single-step reactions, the two discrimination mechanisms are strictly alternative and can not
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minimum error . However, the two modes can be combined in multi-step reactions, such as in models implementing error correction through a proofreading pathway.
error fraction. Close to the lowest error limit, kinetic discrimination results in a diverging copying velocity and dissipation per copied bit. On the opposite, energetic discrimination reaches its lowest error limit in an adiabatic regime where dissipation and velocity vanish.
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seemingly similar
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. Finally, we show how the two mechanisms can be combined in copying schemes implementing error correction through a proofreading pathway