733 research outputs found
DNA unzipped under a constant force exhibits multiple metastable intermediates
Single molecule studies, at constant force, of the separation of
double-stranded DNA into two separated single strands may provide information
relevant to the dynamics of DNA replication. At constant applied force, theory
predicts that the unzipped length as a function of time is characterized by
jumps during which the strands separate rapidly, followed by long pauses where
the number of separated base pairs remains constant. Here, we report previously
uncharacterized observations of this striking behavior carried out on a number
of identical single molecules simultaneously. When several single lphage
molecules are subject to the same applied force, the pause positions are
reproducible in each. This reproducibility shows that the positions and
durations of the pauses in unzipping provide a sequence-dependent molecular
fingerprint. For small forces, the DNA remains in a partially unzipped state
for at least several hours. For larger forces, the separation is still
characterized by jumps and pauses, but the double-stranded DNA will completely
unzip in less than 30 min
Statistical Mechanics of Torque Induced Denaturation of DNA
A unifying theory of the denaturation transition of DNA, driven by
temperature T or induced by an external mechanical torque Gamma is presented.
Our model couples the hydrogen-bond opening and the untwisting of the
helicoidal molecular structure. We show that denaturation corresponds to a
first-order phase transition from B-DNA to d-DNA phases and that the
coexistence region is naturally parametrized by the degree of supercoiling
sigma. The denaturation free energy, the temperature dependence of the twist
angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma
plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve
Getting DNA twist rigidity from single molecule experiments
We use an elastic rod model with contact to study the extension versus
rotation diagrams of single supercoiled DNA molecules. We reproduce
quantitatively the supercoiling response of overtwisted DNA and, using
experimental data, we get an estimation of the effective supercoiling radius
and of the twist rigidity of B-DNA. We find that unlike the bending rigidity,
the twist rigidity of DNA seems to vary widely with the nature and
concentration of the salt buffer in which it is immerged
Twist and writhe dynamics of stiff filaments
This letter considers the dynamics of a stiff filament, in particular the
coupling of twist and bend via writhe. The time dependence of the writhe of a
filament is for a linear filament and for a curved filament. Simulations are used to study the relative
importance of crankshaft motion and tube like motion in twist dynamics.
Fuller's theorem, and its relation with the Berry phase, is reconsidered for
open filamentsComment: 7 Pages with 2 figure
Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA
By resorting to the thick-chain model we discuss how the stretching response
of a polymer is influenced by the self-avoidance entailed by its finite
thickness. The characterization of the force versus extension curve for a thick
chain is carried out through extensive stochastic simulations. The
computational results are captured by an analytic expression that is used to
fit experimental stretching measurements carried out on DNA and single-stranded
RNA (poly-U) in various solutions. This strategy allows us to infer the
apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and
poly-U, for different ionic strengths. Due to the very different degree of
flexibility of the two molecules, the results provide insight into how the
apparent diameter is influenced by the interplay between the
(solution-dependent) Debye screening length and the polymers' ``bare''
thickness. For DNA, the electrostatic contribution to the effective radius,
, is found to be about 5 times larger than the Debye screening length,
consistently with previous theoretical predictions for highly-charged stiff
rods. For the more flexible poly-U chains the electrostatic contribution to
is found to be significantly smaller than the Debye screening length.Comment: iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matte
Dynamics of folding in Semiflexible filaments
We investigate the dynamics of a single semiflexible filament, under the
action of a compressing force, using numerical simulations and scaling
arguments. The force is applied along the end to end vector at one extremity of
the filament, while the other end is held fixed. We find that, unlike in
elastic rods the filament folds asymmetrically with a folding length which
depends only on the bending stiffness and the applied force. It is shown that
this behavior can be attributed to the exponentially falling tension profile in
the filament. While the folding time depends on the initial configuration, at
late time, the distance moved by the terminal point of the filament and the
length of the fold shows a power law dependence on time with an exponent 1/2.Comment: 13 pages, Late
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
Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems
Biomolecules carry out very specialized tasks inside the cell where energies
involved are few tens of k_BT, small enough for thermal fluctuations to be
relevant in many biomolecular processes. In this paper I discuss a few concepts
and present some experimental results that show how the study of fluctuation
theorems applied to biomolecules contributes to our understanding of the
nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India).
Invited contributio
Thermal Fluctuations of Elastic Filaments with Spontaneous Curvature and Torsion
We study the effects of thermal flucutations on thin elastic filaments with
spontaneous curvature and torsion. We derive analytical expressions for the
orientational correlation functions and for the persistence length of helices,
and find that this length varies non-monotonically with the strength of thermal
fluctuations. In the weak fluctuation regime, the persistence length of a
spontaneously twisted helix has three resonance peaks as a function of the
twist rate. In the limit of strong fluctuations, all memory of the helical
shape is lost.Comment: 1 figur
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
- …