  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 motor's 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.
