Modeling enzyme induced creation of bubbles in DNA

The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that in fact from certain local structural distortions there originate oscillating localized patterns, that is radial and torsional breathers, which are associated with localized H-bond deformations, being reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim the underlying nonlinear oscillator network of the DNA duplex is brought in contact with a heat bath using the Nosé-Hoover-method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers, sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for nonzero temperature the H-bond breathers move coherently along the double chain whereas at T = 0 standing radial and torsional breathers result. PACS numbers: 87.-15.v, 63.20.Kr, 63.20.Ry