Biomechanics of DNA: rjtational oscillations of bases
Institute of Cell Biophysics, Russia, 142290, Pushchino, Moscow region, Institutskaya str. 3, (4967)739252, firstname.lastname@example.org pp. (accepted)
Molecule of DNA is a complex biomechanical system including many different types of internal motions. Motions of individual atoms, motions of the atomic groups (sugars, phosphate groups, bases), motions of the polynucleotide chain fragments are among them.
In this work we consider one of the motions: rotational oscillations of the DNA bases forming a pair: Adenine – Thymine (AT) or Guanine- Cytosine (GC). These motions are of special interest because they make an important contribution to formation of the open states? Which, in turn, are play important role in the processes of the DNA-protein recognition.
To make calculations we use the DNA fragment, consisting of three coupled base pairs. It is suggested that the bases of the central pair can oscillate in the horizontal plane (xy) that is orthogonal to the main (vertical) molecule axis (z), and the bases in the other two pairs remain unmovable. In the mechanical analog of the DNA fragment the bases are imitated by pendulums, hydrogen bonds – by horizontal springs connecting pendulums in pairs, stacking interactions – by vertical springs connecting pendulums that belong to the nearest neighboring pairs. Sugar-phosphate chains are considered as rigid and unmoveable. The model takes also into account the helical structure of the DNA molecule.
We derived the function of Lagrange and equations of motion that imitate oscillations of the bases of the central pair. Solutions of the equations are found and the trajectories in the configuration space are constructed
The work has been executed at partial financial support of the grant N 08-04-00197 of the Russian Foundation for Basic Research.