An Interdisciplinary Journal

2007, Vol.10, No.3, pp.228-237

Local Opening of DNA Chain as a Resonance Mode.
Slobodan Zdravković

In this article, the dynamics of a DNA chain is described by the Peyrard-Bishop-Dauxois model. A nucleotide pair oscillates with extremely high amplitude, which is called the resonance mode, when a nonlinear parameter of the nonlinear Schrödinger equation approaches to zero. This is a sort of parametric resonance as if some parameters change in time. It is explained that this could happen during the m-RNA transcription. It is well known that the transcription may happen only if the DNA chain opens locally. It is argued that this local opening of the DNA chain is nothing but the resonance behaviour.

It is also shown that the resonance, that is extremely high amplitude of the nucleotide vibrations, occurs when the frequencies of the in-phase and out-of-phase motions, usually called acoustical and optical frequencies, are equal. This practically means that the surrounding of a particular nucleotide pair might be viewed as an external force. In addition, this gives some information about possible values of a ratio between harmonic constants of the longitudinal and the helicoidal springs.
Key words: DNA dynamics, PBD model, resonance mode

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