Inhomogeneities and nonlinear dynamics of a helical DNA interacting with a RNA-polymerase
| Autor: | Mirabeau Saha, Timoleon Crepin Kofane |
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| Rok vydání: | 2014 |
| Předmět: | |
| Zdroj: | Physica Scripta. 89:085003 |
| ISSN: | 1402-4896 0031-8949 |
| DOI: | 10.1088/0031-8949/89/8/085003 |
| Popis: | We have numerically investigated the effects of helicity and inhomogeneities on DNA base pairs opening. The inhomogeneities are due to the site-dependent stacking and hydrogen bonding energies in DNA and protein molecules. We have considered a situation in which the active site of the RNA-polymerase molecule binds onto the promoter site of the spin-like model of the DNA molecule at the physiological temperature and creates a bubble. During the study, we have found that the helical coupling has to be very weak compared to intra-strand coupling in the real DNA molecule. Results show that inhomogeneities do not affect the general pattern of base pair opening, even as the periodic inhomogeneity introduces a train of periodic oscillations on the tail of the bubble; while the height of the bubble is an increasing function of the helical coupling parameter. The basic properties of breather-like modes, obtained here by taking into account helical structure and inhomogeneities, are essential for DNA functioning since such breathing-like modes are considered to be much better candidates for the nonlinear modes responsible for a locally open state where biological functioning takes place. |
| Databáze: | OpenAIRE |
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