Bubble statistics and dynamics in double-stranded DNA

Abstract

The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two distribution functions describing localized separations ("bubbles") of the double strand. The result that the bubble distributions are more sharply peaked at the active sites than thermodynamically obtained distributions is ascribed to the fact that the bubble lifetimes affect the distributions. Certain base-pair sequences are found to promote long-lived bubbles, and we argue that this is a result of length scale competition between the nonlinearity and disorder present in the system.

Nonlinearity in DNA and its Relation to Specific Functions

“…Similar results were obtained for a number of other viral promoters [24,25]. In particular, it was shown that the large bubbles containing the +1 base pair are also the longest-lived (on average) bubbles [26].…”

Modeling the interaction of DNA with alternating fields

“…Increasing the field amplitude leads to the increase of opening probability at these sites and helps the opening of others. Without the THz field, the opening probability of P5 promoter at the TATA box is higher than at the TSS [31,43]. The most persistent bubbles are found at the sites that have been pointed out before, see Fig.…”

“…It has potential ability to describe the melting transition and denaturation bubbles of the dsDNA such as those that occur during the initial stage of the transcription process. Some specific correlation with transcription initiation sites has been claimed [22,[28][29][30][31] and debated [32,33].…”

Simple combined model for nonlinear excitations in DNA

“…12,13). However, recently it was argued 14,15,16,17,18 that thermodynamic characterization of the thermal fluctuations may differ from a dynamical characterization, which points to the need for a thorough understanding of the dynamical effects in this highly nonlinear and cooperative material.…”