  A model is presented to describe the nucleotide and repeat addition
processivity by the telomerase. In the model, the processive nucleotide
addition is implemented on the basis of two requirements: One is that stem IV
loop stimulates the chemical reaction of nucleotide incorporation, and the
other one is the existence of an ssRNA-binding site adjacent to the polymerase
site that has a high affinity for the unpaired base of the template. The
unpairing of DNA:RNA hybrid after the incorporation of the nucleotide paired
with the last base on the template, which is the prerequisite for repeat
addition processivity, is caused by a force acting on the primer. The force is
resulted from the unfolding of stem III pseudoknot that is induced by the
swinging of stem IV loop towards the nucleotide-bound polymerase site. Based on
the model, the dynamics of processive nucleotide and repeat additions by
Tetrahymena telomerase are quantitatively studied, which give good explanations
to the previous experimental results. Moreover, some predictions are presented.
In particular, it is predicted that the repeat addition processivity is mainly
determined by the difference between the free energy required to disrupt the
DNA:RNA hybrid and that required to unfold the stem III pseudoknot, with the
large difference corresponding to a low repeat addition processivity while the
small one corresponding to a high repeat addition processivity.
