Nonlinear excitations in DNA: Aperiodic models vs actual genome sequences

Details Nonlinear excitations in DNA: Aperiodic models vs actual genome sequences Nonlinear excitations in DNA: Aperiodic models vs actual genome sequences

2004-07-02

arxiv.org/abs/q-bio/0407002v2

Biology

Quantitative Biology

Genomics

Final version, accepted in Physical Review E, minor changes in text, figures improved

Scientific paper

10.1103/PhysRevE.70.051903

We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Dom\'\i nguez-Adame {\em et al.}, Phys. Rev. E {\bf 52}, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent on the specific sequence. The results of our model are consistent with the stick-slip dynamics of the unzipping process observed in experiments. We also show that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A {\bf 193}, 263 (1994)] is a useful tool to identify key regions in DNA that control the dynamical behavior of large segments. Additionally, our results lead to further insights in the phenomenology observed in aperiodic systems.

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