Biomechanics of DNA: rotational oscillations of bases

In this paper we study the rotational oscillations of the nitrous bases forming a central pair in a short DNA fragment consisting of three base pairs. A simple mechanical analog of the fragment where the bases are imitated by pendulums and the interactions between pendulums — by springs, has been constructed. We derived Lagrangian of the model system and the nonlinear equations of motions. We found solutions in the homogeneous case when the fragment considered consists of identical base pairs: Adenine–Thymine (AT-pair) or Guanine–Cytosine (GC-pair). The trajectories of the model system in the configuration space were also constructed.