Simulation of the conformation and dynamics of a double-helical model for DNA

Abstract

We propose a partially flexible, double-helical model for describing the conformational and dynamic properties of DNA. In this model, each nucleotide is represented by one element (bead), and the known geometrical features of the double helix are incorporated in the equilibrium conformation. Each bead is connected to a few neighbor beads in both strands by means of stiff springs that maintain the connectivity but still allow for some extent of flexibility and internal motion. We have used Brownian dynamics simulation to sample the conformational space and monitor the overall and internal dynamics of short DNA pieces, with up to 20 basepairs. From Brownian trajectories, we calculate the dimensions of the helix and estimate its persistence length. We obtain translational diffusion coefficient and various rotational relaxation times, including both overall rotation and internal motion. Although we have not carried out a detailed parameterization of the model, the calculated properties agree rather well with experimental data available for those oligomers.

An ab initio theoretical study of electronic structure and properties of 2′‐deoxyguanosine in gas phase and aqueous media

“…[3][4][5][6] Vigorous efforts are being made to understand the structures and properties of a variety of biomolecules including the nucleic acid bases using theoretical and spectroscopic methods. [3][4][5][6][7][8][9][10][11][12] Electronic structure calculations, 13,14 simulation, 15,16 and studies of solvent effects [17][18][19][20] have been carried out on several systems, including the nucleic acid bases and other biologically important molecules. It is found that behaviors of biomolecules in aqueous media may be appreciably different from those in crystals.…”

Methods and Tools for the Prediction of Hydrodynamic Coefficients and Other Solution Properties of Flexible Macromolecules in Solution. A Tutorial Minireview

“…A simple way is to adopt for $V_{ij}^{({\rm pair})} $ a quadratic form like Equation 2 for the stiff connecting bonds, where now l e would be the equilibrium value of r ij , using a sufficiently high value for the force constant H . This would give rise to what is now called the elastic network model36, 37 of quasi‐rigid proteins, which was indeed proposed earlier to describe the local stiffness of the DNA double helix 38…”

On The Features Solitary Wave Solutions for the DoubleStructures Model of DNA

“…Since the structure of DNA double helix has been discovered by Watson and Crick in 1953 [2]. Many researchers, especially ones in theoretical physics and nonlinear dynamics and also triggered the formulation of several simple models of nonlinear DNA dynamics corresponding to geometric structure, namely, the DNA double-stranded [3][4][5][6][7][8][9][10][11][12][13][14] or the double helix [15][16][17][18][19][20][21][22][23][24][25][26][27][28]. These models had been developed during the past decade to describe the nonlinear dynamics properties of open base-pairs in DNA, which commonly called denaturation bubbles [29].…”