Publication: Nonlinear excitatios in DNA: aperiodic models versus actual genome sequences
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ISSN: 1539-3755 (print version)
ISSN: 1550-2376 (online version)
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2004-11
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American Physical Society
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Abstract
We study the effects of the genetic sequence on the propagation of nonlinear excitations in simple models of
DNA in which we incorporate actual data from the human genome. We show that kink propagation requires
forces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Domínguez-Adame et
al., Phys. Rev. E 52, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent on
the specific sequence. Contrary to the conjecture advanced by Domínguez-Adame and co-workers, we find no
evidence supporting the dependence of the kink dynamics on the information content of the genetic sequences
considered. We discuss possible reasons for that result as well as its practical consequences. Physically, 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 193, 263 (1994)], is a useful tool to identify key regions in DNA that control the
dynamical behavior of large segments. As a side result, we extend the previous studies on aperiodic sequences
by analyzing the effect of the initial position of the kink, leading to further insight on the phenomenology
observed in such systems.
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Physical Review E, vol. 70, n. 5, nov. 2004. Pp. 1-8