ABSTRACT
We study nonlinear dynamics of the DNA molecule relying on a helicoidal Peyrard-Bishop model. We look for traveling wave solutions and show that a continuum approximation brings about kink solitons moving along the chain. This statement is supported by the numerical solution of a relevant dynamical equation of motion. Finally, we argue that an existence of both kinks and localized modulated solitons (breathers) could be a useful tool to describe DNA-RNA transcription.
Subject(s)
DNA/metabolism , Nonlinear Dynamics , Nucleic Acid Conformation , Hydrogen Bonding , Protein Structure, Secondary , Transcription, Genetic/geneticsABSTRACT
Nonlinear dynamics of DNA molecule at segments where DNA-RNA transcription occurs is studied. Our basic idea is that the solitary wave, moving along the chain, transforms into a demodulated one at these segments. The second idea is that the wave becomes a standing one due to interaction with DNA surrounding, e.g., RNA polymerase molecules. We explain why this is biologically convenient and show that our results match the experimental ones. In addition, we suggest how to experimentally determine crucial constant describing covalent bonds within DNA.
