181 research outputs found
Le Nouveau Détective : vers une sociologie de l'énonciation
National audienceLa communication propose de penser l'activité énonciative du Nouveau Détective, seul magazine français entièrement consacré au fait divers à partir du modèle inspiré de la sociologie de l'énonciation : le modèle d'analyse utilisé se fonde sur le principe selon lequel toute énonciation induit trois processus qui concernent respectivement l'appropriation d'un langage, l'enrôlement d'acteurs, la mobilisation d'un monde. Les institutions journalistiques doivent être à la fois en mesure de s'accommoder de ces principes pour attester leur appartenance au champ médiatique et jouer avec ces principes pour marquer leur individualité
Pause Point Spectra in DNA Constant-Force Unzipping
Under constant applied force, the separation of double-stranded DNA into two
single strands is known to proceed through a series of pauses and jumps. Given
experimental traces of constant-force unzipping, we present a method whereby
the locations of pause points can be extracted in the form of a pause point
spectrum. A simple theoretical model of DNA constant-force unzipping is
demonstrated to produce good agreement with the experimental pause point
spectrum of lambda phage DNA. The locations of peaks in the experimental and
theoretical pause point spectra are found to be nearly coincident below 6000
bp. The model only requires the sequence, temperature and a set of empirical
base pair binding and stacking energy parameters, and the good agreement with
experiment suggests that pause points are primarily determined by the DNA
sequence. The model is also used to predict pause point spectra for the
BacterioPhage PhiX174 genome. The algorithm for extracting the pause point
spectrum might also be useful for studying related systems which exhibit
pausing behavior such as molecular motors.Comment: 15 pages, 12 figure
Elasticity of semiflexible polymers with and without self-interactions
A {\it new} formula for the force vs extension relation is derived from the
discrete version of the so called {\it worm like chain} model. This formula
correctly fits some recent experimental data on polymer stretching and some
numerical simulations with pairwise repulsive potentials. For a more realistic
Lennard-Jones potential the agreement with simulations is found to be good when
the temperature is above the temperature. For lower temperatures a
plateau emerges, as predicted by some recent experimental and theoretical
results, and our formula gives good results only in the high force regime. We
briefly discuss how other kinds of self-interactions are expected to affect the
elasticity of the polymer.Comment: 8 pages, 10 figure
Single-molecule derivation of salt dependent base-pair free energies in DNA
Accurate knowledge of the thermodynamic properties of nucleic acids is
crucial to predicting their structure and stability. To date most measurements
of base-pair free energies in DNA are obtained in thermal denaturation
experiments, which depend on several assumptions. Here we report measurements
of the DNA base-pair free energies based on a simplified system, the mechanical
unzipping of single DNA molecules. By combining experimental data with a
physical model and an optimization algorithm for analysis, we measure the 10
unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision
over two orders of magnitude of monovalent salt concentration. We find an
improved set of standard energy values compared with Unified Oligonucleotide
energies and a unique set of 10 base-pair-specific salt-correction values. The
latter are found to be strongest for AA/TT and weakest for CC/GG. Our new
energy values and salt corrections improve predictions of DNA unzipping forces
and are fully compatible with melting temperatures for oligos. The method
should make it possible to obtain free energies, enthalpies and entropies in
conditions not accessible by bulk methodologies.Comment: Main text: 27 pages, 4 figures, 2 tables. Supporting Information: 51
pages, 19 figures, 4 table
Theory of biopolymer stretching at high forces
We provide a unified theory for the high force elasticity of biopolymers
solely in terms of the persistence length, , and the monomer spacing,
. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely
Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the
Worm-like Chain (WLC) is a better model. We show that can be estimated
from the force extension curve (FEC) at the extension
(normalized by the contour length of the biopolymer). After validating the
theory using simulations, we provide a quantitative analysis of the FECs for a
diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and
unstructured PEVK domain of titin) for . The success of a specific
polymer model (FJC or WLC) to describe the FEC of a given biopolymer is
naturally explained by the theory. Only by probing the response of biopolymers
over a wide range of forces can the -dependent elasticity be fully
described.Comment: 20 pages, 4 figure
Mesoscopic models for DNA stretching under force: new results and comparison to experiments
Single molecule experiments on B-DNA stretching have revealed one or two
structural transitions, when increasing the external force. They are
characterized by a sudden increase of DNA contour length and a decrease of the
bending rigidity. It has been proposed that the first transition, at forces of
60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA,
while the second one, at stronger forces, is a strand peeling resulting in
single stranded DNAs (ssDNA), similar to thermal denaturation. But due to
experimental conditions these two transitions can overlap, for instance for
poly(dA-dT). We derive analytical formula using a coupled discrete worm like
chain-Ising model. Our model takes into account bending rigidity, discreteness
of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit
of zero force, this model simplifies into a coupled model already developed by
us for studying thermal DNA melting, establishing a connexion with previous
fitting parameter values for denaturation profiles. We find that: (i) ssDNA is
fitted, using an analytical formula, over a nanoNewton range with only three
free parameters, the contour length, the bending modulus and the monomer size;
(ii) a surprisingly good fit on this force range is possible only by choosing a
monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase
length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss)
transitions; (iv) an analytical formula for fitting B to S transitions is
derived in the strong force approximation and for long DNAs, which is in
excellent agreement with exact transfer matrix calculations; (v) this formula
fits perfectly well poly(dG-dC) and -DNA force-extension curves with
consistent parameter values; (vi) a coherent picture, where S to ssDNA
transitions are much more sensitive to base-pair sequence than the B to S one,
emerges.Comment: 14 pages, 9 figure
DNA mechanics as a tool to probe helicase and translocase activity
Helicases and translocases are proteins that use the energy derived from ATP hydrolysis to move along or pump nucleic acid substrates. Single molecule manipulation has proved to be a powerful tool to investigate the mechanochemistry of these motors. Here we first describe the basic mechanical properties of DNA unraveled by single molecule manipulation techniques. Then we demonstrate how the knowledge of these properties has been used to design single molecule assays to address the enzymatic mechanisms of different translocases. We report on four single molecule manipulation systems addressing the mechanism of different helicases using specifically designed DNA substrates: UvrD enzyme activity detection on a stretched nicked DNA molecule, HCV NS3 helicase unwinding of a RNA hairpin under tension, the observation of RecBCD helicase/nuclease forward and backward motion, and T7 gp4 helicase mediated opening of a synthetic DNA replication fork. We then discuss experiments on two dsDNA translocases: the RuvAB motor studied on its natural substrate, the Holliday junction, and the chromosome-segregation motor FtsK, showing its unusual coupling to DNA supercoiling
Single-molecule imaging of Bacteroides fragilis AddAB reveals the highly processive translocation of a single motor helicase
The AddAB helicase and nuclease complex is used for repairing double-strand DNA breaks in the many bacteria that do not possess RecBCD. Here, we show that AddAB, from the Gram-negative opportunistic pathogen Bacteroides fragilis, can rescue the ultraviolet sensitivity of an Escherichia coli recBCD mutant and that addAB is required for survival of B. fragilis following DNA damage. Using single-molecule observations we demonstrate that AddAB can translocate along DNA at up to 250 bp per second and can unwind an average of 14 000 bp, with some complexes capable of unwinding 40 000 bp. These results demonstrate the importance of processivity for facilitating encounters with recognition sequences that modify enzyme function during homologous recombination
- …