128 research outputs found
Denaturation of Heterogeneous DNA
The effect of heterogeneous sequence composition on the denaturation of
double stranded DNA is investigated. The resulting pair-binding energy
variation is found to have a negligible effect on the critical properties of
the smooth second order melting transition in the simplest (Peyrard-Bishop)
model. However, sequence heterogeneity is dramatically amplified upon adopting
a more realistic treatment of the backbone stiffness. The model yields features
of ``multi-step melting'' similar to those observed in experiments.Comment: 4 pages, LaTeX, text and figures also available at
http://matisse.ucsd.edu/~hw
Roles of stiffness and excluded volume in DNA denaturation
The nature and the universal properties of DNA thermal denaturation are
investigated by Monte Carlo simulations. For suitable lattice models we
determine the exponent c describing the decay of the probability distribution
of denaturated loops of length l, . If excluded volume effects
are fully taken into account, c= 2.10(4) is consistent with a first order
transition. The stiffness of the double stranded chain has the effect of
sharpening the transition, if it is continuous, but not of changing its order
and the value of the exponent c, which is also robust with respect to inclusion
of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as
publishe
Order of the phase transition in models of DNA thermal denaturation
We examine the behavior of a model which describes the melting of
double-stranded DNA chains. The model, with displacement-dependent stiffness
constants and a Morse on-site potential, is analyzed numerically; depending on
the stiffness parameter, it is shown to have either (i) a second-order
transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2
(characteristic of short range attractive part of the Morse potential) or (ii)
a first-order transition with finite melting entropy, discontinuous fraction of
bound pairs, divergent correlation lengths, and critical exponents
"nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in
Phys. Rev. Let
Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
The paper uses mesoscopic, non-linear lattice dynamics based
(Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA
below and near the denaturation temperature. Computationally efficient notation
is introduced for the relevant statistical mechanics. Computed melting profiles
of long and short heterogeneous sequences are presented, using a recently
introduced reparametrization of the PBD model, and critically discussed. The
statistics of extended open bubbles and bound clusters is formulated and
results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical
Physics (ed. G. Gaeta
Multiple timescales in a model for DNA denaturation dynamics
The denaturation dynamics of a long double-stranded DNA is studied by means
of a model of the Poland-Scheraga type. We note that the linking of the two
strands is a locally conserved quantity, hence we introduce local updates that
respect this symmetry. Linking dissipation via untwist is allowed only at the
two ends of the double strand. The result is a slow denaturation characterized
by two time scales that depend on the chain length . In a regime up to a
first characteristic time the chain embodies an
increasing number of small bubbles. Then, in a second regime, bubbles coalesce
and form entropic barriers that effectively trap residual double-stranded
segments within the chain, slowing down the relaxation to fully molten
configurations, which takes place at . This scenario is
different from the picture in which the helical constraints are neglected.Comment: 9 pages, 5 figure
Bubble propagation in a helicoidal molecular chain
We study the propagation of very large amplitude localized excitations in a
model of DNA that takes explicitly into account the helicoidal structure. These
excitations represent the ``transcription bubble'', where the hydrogen bonds
between complementary bases are disrupted, allowing access to the genetic code.
We propose these kind of excitations in alternative to kinks and breathers. The
model has been introduced by Barbi et al. [Phys. Lett. A 253, 358 (1999)], and
up to now it has been used to study on the one hand low amplitude breather
solutions, and on the other hand the DNA melting transition. We extend the
model to include the case of heterogeneous chains, in order to get closer to a
description of real DNA; in fact, the Morse potential representing the
interaction between complementary bases has two possible depths, one for A-T
and one for G-C base pairs. We first compute the equilibrium configurations of
a chain with a degree of uncoiling, and we find that a static bubble is among
them; then we show, by molecular dynamics simulations, that these bubbles, once
generated, can move along the chain. We find that also in the most unfavourable
case, that of a heterogeneous DNA in the presence of thermal noise, the
excitation can travel for well more 1000 base pairs.Comment: 25 pages, 7 figures. Submitted to Phys. Rev.
Why is the DNA Denaturation Transition First Order?
We study a model for the denaturation transition of DNA in which the
molecules are considered as composed of a sequence of alternating bound
segments and denaturated loops. We take into account the excluded-volume
interactions between denaturated loops and the rest of the chain by exploiting
recent results on scaling properties of polymer networks of arbitrary topology.
The phase transition is found to be first order in d=2 dimensions and above, in
agreement with experiments and at variance with previous theoretical results,
in which only excluded-volume interactions within denaturated loops were taken
into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let
A Simple Model for the DNA Denaturation Transition
We study pairs of interacting self-avoiding walks on the 3d simple cubic
lattice. They have a common origin and are allowed to overlap only at the same
monomer position along the chain. The latter overlaps are indeed favored by an
energetic gain.
This is inspired by a model introduced long ago by Poland and Sheraga [J.
Chem. Phys. {\bf 45}, 1464 (1966)] for the denaturation transition in DNA
where, however, self avoidance was not fully taken into account. For both
models, there exists a temperature T_m above which the entropic advantage to
open up overcomes the energy gained by forming tightly bound two-stranded
structures.
Numerical simulations of our model indicate that the transition is of first
order (the energy density is discontinuous), but the analog of the surface
tension vanishes and the scaling laws near the transition point are exactly
those of a second order transition with crossover exponent \phi=1. Numerical
and exact analytic results show that the transition is second order in modified
models where the self-avoidance is partially or completely neglected.Comment: 29 pages, LaTeX, 20 postscript figure
Depinning of semiflexible polymers in (1+1) dimensions
We present a theoretical analysis of a simple model of the depinning of an
anchored semiflexible polymer from a fixed planar substrate in (1+1)
dimensions. We consider a polymer with a discrete sequence of pinning sites
along its contour. Using the scaling properties of the conformational
distribution function in the stiff limit and applying the necklace model of
phase transitions in quasi-one-dimensional systems, we obtain a melting
criterion in terms of the persistence length, the spacing between pinning
sites, a microscopic effective length which characterizes a bond, and the bond
energy. The limitations of this and other similar approaches are also
discussed. In the case of force-induced unbinding, it is shown that the bending
rigidity favors the unbinding through a ``lever-arm effect''
Cross Priming Amplification: Mechanism and Optimization for Isothermal DNA Amplification
CPA is a class of isothermal amplification reactions that is carried out by a strand displacement DNA polymerase and does not require an initial denaturation step or the addition of a nicking enzyme. At the assay temperature of 63°C, the formation of a primer-template hybrid at transient, spontaneous denaturation bubbles in the DNA template is favored over re-annealing of the template strands by the high concentration of primer relative to template DNA. Strand displacement is encouraged by the annealing of cross primers with 5′ ends that are not complementary to the template strand and the binding of a displacement primer upstream of the crossing primer. The resulting exponential amplification of target DNA is highly specific and highly sensitive, producing amplicons from as few as four bacterial cells. Here we report on the basic CPA mechanism – single crossing CPA – and provide details on alternative mechanisms
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