Bending and twisting dynamics of short linear DNAs. Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation

Abstract

Brownian dynamics is used to simulate the decay anisotropy of short linear DNA fragments modeled as a string of beads. The model is sufficiently general to allow for static bends, anisotropic bending, and elastic constants for bending and twisting which can vary along the chain. In limiting cases, simulations are found to be in excellent agreement with analytic theory down to a correlation length of at least 500 Å. This model is then used to analyze the 0–2.5 μs triplet depletion anisotropy decay of a 209 base pair sea urchin DNA fragment. It is concluded that the conventional worm-like chain model, in which bending is isotropic and/or there are no static bends along the chain, is unable to account for the experimental results unless a correlation length of 1000 Å is assumed. A worm-like chain with anisotropic bending requires a similar but slightly larger correlation length.

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition

“…Although basic features of the model are similar to those of the Allison and Langowski groups (Allison et al, 1989(Allison et al, , 1990Chirico & Langowski, 1996;Heath et al, 1996;Hammermann et al, 1997) some details, such as the electrostatic interaction among DNA segments, are treated differently. We also improved performance of the BD algorithm so that longer trajectories can be simulated for the same accuracy and computer time.…”

“…Our DNA model is based on the discrete worm-like chain similar to one developed by Allison et al (Allison et al, 1989;Allison, 1986;Allison & McCammon, 1984) and extended later by Chirico & Langowskii for the case of supercoiled DNA (Chirico & Langowski, 1994, 1996. A careful adaptation, parameterization and testing for linear DNA was described by Jian et al (1997).…”

“…One of these approaches, based on BD (Ermak & McCammon, 1978), is most suitable to study the slow process of site juxtaposition. It has been shown that BD allows accurate quantitative description of both equilibrium and transport properties of DNA molecules (Allison et al, 1989(Allison et al, , 1990Allison, 1986;Chirico & Langowski, 1992. Furthermore, conformational changes over large time intervals can be simulated.…”

Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study

“…Twist-bend coupling, which allows the model to capture the effects of superhelicity upon the dynamics, enters through a set of torsional forces that result from the independence of the infinitesimal coordinates of the beads. 15,19 The BD bead-chain representation of dsDNA has, for equilibrium systems involving free linear DNA and statically-stressed superhelical ccDNA, predicted with reasonable accuracy such observable parameters as decay anisotropy measured by fluorescence depolarization and triplet anisotropy decay, 14 translational and rotational diffusion coefficients measured by dynamic light scattering, 15 and ring closure probablities measured in cyclization reaction experiments. 20 Our results demonstrate that the present model captures several significant features of transcriptional twin supercoiling, and, more generally, elucidates the nonequilibrium response of DNA to dynamically imposed torsional stress, suggesting its potential as a tool for analysis of solvent-mediated dynamic supercoiling under a wide range of conditions and circumstances.…”

Efficient simulation of semiflexible polymers

“…We found reports of time steps of 12.9 ps [36], 5 ps [37], and 3.8 ps [38], in simulations in which a bead represents 4, 9, and 37 base pairs, respectively. A back-of-the-envelope estimate then yields that, by and large, these time steps are below the maximal time step estimated by us for an integration scheme in real-space coordinates.…”