598 research outputs found
Monte Carlo implementation of supercoiled double-stranded DNA
Metropolis Monte Carlo simulation is used to investigate the elasticity of
torsionally stressed double-stranded DNA, in which twist and supercoiling are
incorporated as a natural result of base-stacking interaction and backbone
bending constrained by hydrogen bonds formed between DNA complementary
nucleotide bases. Three evident regimes are found in extension versus torsion
and/or force versus extension plots: a low-force regime in which over- and
underwound molecules behave similarly under stretching; an intermediate-force
regime in which chirality appears for negatively and positively supercoiled DNA
and extension of underwound molecule is insensitive to the supercoiling degree
of the polymer; and a large-force regime in which plectonemic DNA is fully
converted to extended DNA and supercoiled DNA behaves quite like a torsionless
molecule. The striking coincidence between theoretic calculations and recent
experimental measurement of torsionally stretched DNA [Strick et al., Science
{\bf 271}, 1835 (1996), Biophys. J. {\bf 74}, 2016 (1998)] strongly suggests
that the interplay between base-stacking interaction and permanent
hydrogen-bond constraint takes an important role in understanding the novel
properties of elasticity of supercoiled DNA polymer.Comment: 21 pages, 6 PS figures. To appear at Biophys.
Theoretical models of DNA topology simplification by type IIA DNA topoisomerases
It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology—the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the enzymes made clear biological sense, it was not clear how small enzymes could selectively change the topology of very large DNA molecules, since topology is a global property and cannot be determined by a local DNA–protein interaction. A few models, suggested to explain the phenomenon, are analyzed in this review. We also consider experimental data that both support and contravene these models
Non-equilibrium hydrodynamics of a rotating filament
The nonlinear dynamics of an elastic filament that is forced to rotate at its
base is studied by hydrodynamic simulation techniques; coupling between
stretch, bend, twist elasticity and thermal fluctuations is included. The
twirling-overwhirling transition is located and found to be strongly
discontinuous. For finite bend and twist persistence length, thermal
fluctuations lower the threshold rotational frequency, for infinite persistence
length the threshold agrees with previous analytical predictions
Comment on "Elasticity Model of a Supercoiled DNA Molecule"
We perform simulations to numerically study the writhe distribution of a
stiff polymer. We compare with analytic results of Bouchiat and Mezard (PRL 80
1556- (1998); cond-mat/9706050).Comment: 1 page, 1 figure revtex
Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix
Under supercoiling constraints, naked DNA, such as a large part of bacterial
DNA, folds into braided structures called plectonemes. The double-helix can
also undergo local structural transitions, leading to the formation of
denaturation bubbles and other alternative structures. Various polymer models
have been developed to capture these properties, with Monte-Carlo (MC)
approaches dedicated to the inference of thermodynamic properties. In this
chapter, we explain how to perform such Monte-Carlo simulations, following two
objectives. On one hand, we present the self-avoiding supercoiled Worm-Like
Chain (ssWLC) model, which is known to capture the folding properties of
supercoiled DNA, and provide a detailed explanation of a standard MC simulation
method. On the other hand, we explain how to extend this ssWLC model to include
structural transitions of the helix.Comment: Book chapter to appear in The Bacterial Nucleoid, Methods and
Protocols, Springer serie
Diffusion of a ring polymer in good solution via the Brownian dynamics
Diffusion constants D_{R} and D_{L} of ring and linear polymers of the same
molecular weight in a good solvent, respectively, have been evaluated through
the Brownian dynamics with hydrodynamic interaction. The ratio ,
which should be universal in the context of the renormalization group, has been
estimated as for the large-N limit. It should be consistent
with that of synthetic polymers, while it is smaller than that of DNAs such as
. Furthermore, the probability of the ring polymer being a
nontrivial knot is found to be very small, while bond crossings may occur at
almost all time steps in the present simulation that realizes the good solvent
conditions.Comment: 11 pages, 4 figure
Elasticity and electrostatics of plectonemic DNA
We present a self-contained theory for the mechanical response of DNA in
single molecule experiments. Our model is based on a 1D continuum description
of the DNA molecule and accounts both for its elasticity and for DNA-DNA
electrostatic interactions. We consider the classical loading geometry used in
experiments where one end of the molecule is attached to a substrate and the
other one is pulled by a tensile force and twisted by a given number of turns.
We focus on configurations relevant to the limit of a large number of turns,
which are made up of two phases, one with linear DNA and the other one with
superhelical DNA. The model takes into account thermal fluctuations in the
linear phase and electrostatic interactions in the superhelical phase. The
values of the torsional stress, of the supercoiling radius and angle, and key
features of the experimental extension-rotation curves, namely the slope of the
linear region and thermal buckling threshold, are predicted. They are found in
good agreement with experimental data.Comment: 19 pages and 6 figure
Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness
DNA and other biopolymers differ from classical polymers due to their
torsional stiffness. This property changes the statistical character of their
conformations under tension from a classical random walk to a problem we call
the `torsional directed walk'. Motivated by a recent experiment on single
lambda-DNA molecules [Strick et al., Science 271 (1996) 1835], we formulate the
torsional directed walk problem and solve it analytically in the appropriate
force regime. Our technique affords a direct physical determination of the
microscopic twist stiffness C and twist-stretch coupling D relevant for DNA
functionality. The theory quantitatively fits existing experimental data for
relative extension as a function of overtwist over a wide range of applied
force; fitting to the experimental data yields the numerical values C=120nm and
D=50nm. Future experiments will refine these values. We also predict that the
phenomenon of reduction of effective twist stiffness by bend fluctuations
should be testable in future single-molecule experiments, and we give its
analytic form.Comment: Plain TeX, harvmac, epsf; postscript available at
http://dept.physics.upenn.edu/~nelson/index.shtm
Nonlinear Mechanical Response of DNA due to Anisotropic Bending Elasticity
The response of a short DNA segment to bending is studied, taking into
account the anisotropy in the bending rigidities caused by the double-helical
structure. It is shown that the anisotropy introduces an effective nonlinear
twist-bend coupling that can lead to the formation of kinks and modulations in
the curvature and/or in the twist, depending on the values of the elastic
constants and the imposed deflection angle. The typical wavelength for the
modulations, or the distance between the neighboring kinks is found to be set
by half of the DNA pitch.Comment: 4 pages, 3 encapsulated EPS figure
Conformations of Linear DNA
We examine the conformations of a model for under- and overwound DNA. The
molecule is represented as a cylindrically symmetric elastic string subjected
to a stretching force and to constraints corresponding to a specification of
the link number. We derive a fundamental relation between the Euler angles that
describe the curve and the topological linking number. Analytical expressions
for the spatial configurations of the molecule in the infinite- length limit
were obtained. A unique configuraion minimizes the energy for a given set of
physical conditions. An elastic model incorporating thermal fluctuations
provides excellent agreement with experimental results on the plectonemic
transition.Comment: 5 pages, RevTeX; 6 postscript figure
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