A three dimensional (3-D) physical model of DNA polymerase movement in DNA replication

In this study, we propose new concepts of Active Potential Energy Well, Specificity and Non-Specificity of the wells. We perform these concepts to establish a 3-D physical model and to elucidate how a complete functional DNA polymerase traps a deoxyribonucleoside triphosphate, and how it moves along a DNA template strand in the elongation of a DNA replication. In our model, we first introduce concepts of reduced mass and relative coordinates of a two objects system. Then we simplify a DNA polymerase movement in DNA replication. We also introduce concepts of active objects and active controls in this study. Our model is based on quantum mechanics, thermal dynamics and published biochemical data.