Model for forward polymerization and switching transition between polymerase and exonuclease sites by DNA polymerase molecular motors

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Abstract

Based on the available crystal structure a model is presented for the polymerization activity and switching transition between polymerase and exonuclease sites of a DNA polymerase molecular motor. Using the model, the fast polymerization rate for correctly base-paired DNA and much reduced polymerization rate after an incorporation of a mismatched base can be well explained. The dependences of the polymerization rate and exonuclease rate on mechanical tension acting on the DNA template are studied. The switching rates between the two sites are analyzed. All the results show good quantitative agreement with the available experimental results.

Section snippets

Model

Similar to the case that monomeric DNA helicases such as Rep and PcrA have a high affinity for the polar ssDNA [18], [19], we assume that there exist two ssDNA-binding sites in the DNA polymerase, one locating in the finger domain and having a high affinity for 5–3ssDNA, while the other one locating in the proofreading domain and having a high affinity for 3–5ssDNA. Besides these two ssDNA-binding sites, there should also exist dsDNA-binding sites in the palm and thumb domains. For example,

Results

Based on the model presented in the above section, the chemical reaction pathway of a DNA polymerase is shown in Fig. 3, which is similar to that given in the literature [2], [14]. The pathway consists mainly of three parts: the chemical reactions related to the polymerization, i.e., the transitions 3  4  5  6  7  3′, the reactions related to the switching transition between polymerase and exonuclease sites and the exonucleolysis, i.e., the transitions 3′  2  2′  3, and the reactions related to the

Discussion

To study the mechanical tension effect on the polymerization rate, the previous models only take into account that one step that involves the rotation of the fingers from “open” to “close” conformations was influenced by the mechanical tension. However, in our present model, two steps that involve the conformational changes near the polymerase site are affected by the mechanical tension on DNA template. One step involves the inward rotation of the fingers and the other step involves the outward

Concluding remarks

A model is presented for polymerization activity and switching transition between polymerase and exonuclease sites of a DNA polymerase molecular motor. Using the model, the fast polymerization rate for correctly base-paired DNA and much reduced polymerization rate after an incorporation of a mismatched base can be well explained. The switching rates between the two sites are quantitatively analyzed. The dependence of polymerization rate and the exonuclease rate on mechanical tension acting on

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