Multi-site H-bridge breathers in DNA

We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi–site breathers in DNA. Within a network model of the DNA double helix we take individual motions of the bases within the base pair plane into account. The resulting H-bridge deformations may be asymmetric with respect to the helix axis. Furthermore the covalent bonds may be deformed distinctly in the two backbone strands. We study the energy exchange processes related with the relaxation dynamics for DNA molecules which have been brought into a non-equilibrium conformation. It is demonstrated that the twist-opening relaxation dynamics of a radially distorted double helix attains an equilibrium regime characterized by a multi-site H-bridge breather. Such a breathing state involves 15 − 20 consecutive base pairs which is a characteristic extension of the experimentally observed oscillating bubbles in DNA.