Published February 18, 2016
| Version v1
Publication
Modeling the thermal evolution of enzyme-created bubbles in DNA
Creators
Contributors
Description
The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes
such as DNA replication, recombination, telomere formation and nucleotide excision repair,
as well as RNA transcription and splicing. These processes 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, 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 into contact with a heat bath using the Nose´–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 non-zero
temperature, the H-bond breathers move coherently along the double chain, whereas at TZ0
standing radial and torsional breathers result.
Additional details
Identifiers
- URL
- https://idus.us.es/handle/11441/35143
- URN
- urn:oai:idus.us.es:11441/35143