Bubble propagation in a helicoidal molecular chain

We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the “transcription bubble,” where the hydrogen bonds between complementary bases are disrupted, allowing access to the genetic code. We propose these kinds of excitations in alternative to kinks and breathers. The model has been introduced by Barbi et al. [Phys. Lett. A 253, 358 (1999)], and up to now it has been used to study on the one hand low amplitude breather solutions, and on the other hand the DNA melting transition. We extend the model to include the case of heterogeneous chains, in order to get closer to a description of real DNA; in fact, the Morse potential representing the interaction between complementary bases has two possible depths, one for $A–T$ and one for $G–C$ base pairs. We first compute the equilibrium configurations of a chain with a degree of uncoiling, and we find that a static bubble is among them; then we show, by molecular dynamics simulations, that these bubbles, once generated, can move along the chain. We find that also in the most unfavorable case, that of a heterogeneous DNA in the presence of thermal noise, the excitation can travel for well more than 1000 base pairs.