3,256 research outputs found
Stretching and relaxation dynamics in double stranded DNA
We study numerically the mechanical stability and elasticity properties of
duplex DNA molecules within the frame of a network model incorporating
microscopic degrees of freedom related with the arrangement of the base pairs.
We pay special attention to the opening-closing dynamics of double-stranded DNA
molecules which are forced into non-equilibrium conformations. Mechanical
stress imposed at one terminal end of the DNA molecule brings it into a
partially opened configuration. We examine the subsequent relaxation dynamics
connected with energy exchange processes between the various degrees of freedom
and structural rearrangements leading to complete recombination to the
double-stranded conformation. The similarities and differences between the
relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are
discussed in detail. In this way we show that the attainment of a
quasi-equilibrium regime proceeds faster in the case of the twisted DNA form
than for its thus less flexible ladder counterpart. Furthermore we find that
the velocity of the complete recombination of the DNA molecule is lower than
the velocity imposed by the forcing unit which is in compliance with the
experimental observations for the opening-closing cycle of DNA molecules.Comment: 21 pages, 9 figure
Comment on "Why is the DNA denaturation transition first order?"
In this comment we argue that while the conclusions in the original paper (Y.
Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct
for asymptotically long DNA chains, they do not apply to the chains used in
typical experiments. In the added last paragraph, we point out that for real
DNA the average distance between denatured loops is not of the order of the
persistence length of a single-stranded chain but much larger. This
corroborates our reasoning that the double helix between loops is quite rigid,
and thereby our conclusion.Comment: 1 page, REVTeX. Last paragraph adde
Elasticity model of a supercoiled DNA molecule
Within a simple elastic theory, we study the elongation versus force
characteristics of a supercoiled DNA molecule at thermal equilibrium in the
regime of small supercoiling. The partition function is mapped to the path
integral representation for a quantum charged particle in the field of a
magnetic monopole with unquantized charge.
We show that the theory is singular in the continuum limit and must be
regularised at an intermediate length scale. We find good agreement with
existing experimental data, and point out how to measure the twist rigidity
accurately.Comment: Latex, 4 pages. The figure contains new experimental data, giving a
new determination of the twist rigidit
Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers
that condense into a compact structure. We use optical tweezers to pull
condensed fibers and investigate the decondensation transition by measuring
force-extension curves (FECs). A characteristic plateau force (around 10 pN)
and hysteresis between the pulling and relaxation cycles are observed for
different dendrimer sizes, indicating the existence of a first-order transition
between two phases (condensed and extended) of the fiber. The fact that we can
reproduce the same FECs in the absence of additional dendrimers in the buffer
medium indicates that dendrimers remain irreversibly bound to the DNA backbone.
Upon salt variation FECs change noticeably confirming that electrostatic forces
drive the condensation transition. Finally, we propose a simple model for the
decondensing transition that qualitatively reproduces the FECs and which is
confirmed by AFM images.Comment: Latex version, 4 pages+3 color 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
Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer
Simple expressions for the bending and the base-stacking energy of
double-stranded semiflexible biopolymers (such as DNA and actin) are derived.
The distribution of the folding angle between the two strands is obtained by
solving a Schr\"{o}dinger equation variationally. Theoretical results based on
this model on the extension versus force and extension versus degree of
supercoiling relations of DNA chain are in good agreement with the experimental
observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it
et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it
ibid.} {\bf 271}, 1835 (1996)].Comment: 8 pages in Revtex format, with 4 EPS figure
Force Spectroscopy with Dual-Trap Optical Tweezers: Molecular Stiffness Measurements and Coupled Fluctuations Analysis
ABSTRACT Dual-trap optical tweezers are often used in high-resolution measurements in single-molecule biophysics. Such measurements can be hindered by the presence of extraneous noise sources, the most prominent of which is the coupling of fluctuations along different spatial directions, which may affect any optical tweezers setup. In this article, we analyze, both from the theoretical and the experimental points of view, the most common source for these couplings in dual-trap optical-tweezers setups: the misalignment of traps and tether. We give criteria to distinguish different kinds of misalignment, to estimate their quantitative relevance and to include them in the data analysis. The experimental data is obtained in a, to our knowledge, novel dual-trap optical-tweezers setup that directly measures forces. In the case in which misalignment is negligible, we provide a method to measure the stiffness of traps and tether based on variance analysis. This method can be seen as a calibration technique valid beyond the linear trap region. Our analysis is then employed to measure the persistence length of dsDNA tethers of three different lengths spanning two orders of magnitude. The effective persistence length of such tethers is shown to decrease with the contour length, in accordance with previous studies
Unzipping Dynamics of Long DNAs
The two strands of the DNA double helix can be `unzipped' by application of
15 pN force. We analyze the dynamics of unzipping and rezipping, for the case
where the molecule ends are separated and re-approached at constant velocity.
For unzipping of 50 kilobase DNAs at less than about 1000 bases per second,
thermal equilibrium-based theory applies. However, for higher unzipping
velocities, rotational viscous drag creates a buildup of elastic torque to
levels above kBT in the dsDNA region, causing the unzipping force to be well
above or well below the equilibrium unzipping force during respectively
unzipping and rezipping, in accord with recent experimental results of Thomen
et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect
of sequence on unzipping and rezipping, and the transient delay in buildup of
the unzipping force due to the approach to the steady state.Comment: 15 pages Revtex file including 9 figure
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