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Register a new userKinetic discrimination of a polymerase in the presence of obstacles
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One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which simultaneously copies a single stranded RNA and opens a single- to double-stranded junction serving as an obstacle. The presence of the obstacle slows down the motor, resulting in a change of its fidelity, which can be used to gain information about the motor and junction dynamics. We find that the motors fidelity does not depend on details of the motor-junction interaction, such as whether the interaction is passive or active. Analysis of the copying fidelity can still be used as a tool for investigating the junction kinetics.
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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 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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