Thermal and mechanical properties of a DNA model with solvation barrier

Abstract

We study the thermal and mechanical behaviors of DNA denaturation in the frame of the mesoscopic Peyrard-Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the principal component analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.

Mesoscopic model for free-energy-landscape analysis of DNA sequences

“…It has been proved [15] that the first few eigenvectors unveil the softest regions of the DNA chain and hence the possible binding sites for our particle. Even more, PCA reduces the large number of degrees of freedom of the system to just a few, by projecting the coordinates of the system into the first few eigenspaces (reduced trajectories).…”

“…where the first term accounts for the hydrogen bond interaction and the second one for interactions with the solvent [15,16]. It was shown in [15] that the inclusion of this barrier modifies drastically the duration and stability of the bubbles.…”

“…It was shown in [15] that the inclusion of this barrier modifies drastically the duration and stability of the bubbles. The potential W (y n , y n−1 ) describes the stacking interaction between the base pairs along the DNA strand,…”

“…Since it has been reported that 1D diffusion periods cover a time of the order of milliseconds [18,19], the simulation time used is reasonable for the problem considered here. The simulation temperature is T = 290K and the boundary conditions for the protein are periodic, while for the chain we consider the hard boundary conditions discussed in [15]. An example of such a trajectory is given in Fig.…”

“…We describe the DNA chain by a modified PeyrardBishop-Dauxois model [13][14][15]. There, the complexity of the DNA molecule is reduced to the study of the dynamics of N base pairs described by the variables y n defining the distance between the bases.…”