287 research outputs found
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
Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness
We characterize the equilibrium thermodynamics of a thick polymer confined in
a spherical region of space. This is used to gain insight into the DNA
packaging process. The experimental reference system for the present study is
the recent characterization of the loading process of the genome inside the
29 bacteriophage capsid. Our emphasis is on the modelling of
double-stranded DNA as a flexible thick polymer (tube) instead of a
beads-and-springs chain. By using finite-size scaling to extrapolate our
results to genome lengths appropriate for 29, we find that the
thickness-induced force may account for up to half the one measured
experimentally at high packing densities. An analogous agreement is found for
the total work that has to be spent in the packaging process. Remarkably, such
agreement can be obtained in the absence of any tunable parameters and is a
mere consequence of the DNA thickness. Furthermore, we provide a quantitative
estimate of how the persistence length of a polymer depends on its thickness.
The expression accounts for the significant difference in the persistence
lengths of single- and double-stranded DNA (again with the sole input of their
respective sections and natural nucleotide/base-pair spacing).Comment: 9 pages, 6 eps figure
Tight and loose shapes in flat entangled dense polymers
We investigate the effects of topological constraints (entanglements) on two
dimensional polymer loops in the dense phase, and at the collapse transition
(Theta point). Previous studies have shown that in the dilute phase the
entangled region becomes tight, and is thus localised on a small portion of the
polymer. We find that the entropic force favouring tightness is considerably
weaker in dense polymers. While the simple figure-eight structure, created by a
single crossing in the polymer loop, localises weakly, the trefoil knot and all
other prime knots are loosely spread out over the entire chain. In both the
dense and Theta conditions, the uncontracted knot configuration is the most
likely shape within a scaling analysis. By contrast, a strongly localised
figure-eight is the most likely shape for dilute prime knots. Our findings are
compared to recent simulations.Comment: 8 pages, 5 figure
Characteristic length of random knotting for cylindrical self-avoiding polygons
We discuss the probability of random knotting for a model of self-avoiding
polygons whose segments are given by cylinders of unit length with radius .
We show numerically that the characteristic length of random knotting is
roughly approximated by an exponential function of the chain thickness .Comment: 5 pages, 4 figure
Mechanical response of plectonemic DNA: an analytical solution
We consider an elastic rod model for twisted DNA in the plectonemic regime.
The molecule is treated as an impenetrable tube with an effective, adjustable
radius. The model is solved analytically and we derive formulas for the contact
pressure, twisting moment and geometrical parameters of the supercoiled region.
We apply our model to magnetic tweezer experiments of a DNA molecule subjected
to a tensile force and a torque, and extract mechanical and geometrical
quantities from the linear part of the experimental response curve. These
reconstructed values are derived in a self-contained manner, and are found to
be consistent with those available in the literature.Comment: 14 pages, 4 figure
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
Interplay of DNA supercoiling and catenation during the segregation of sister duplexes
The discrete regulation of supercoiling, catenation and knotting by DNA topoisomerases is well documented both in vivo and in vitro, but the interplay between them is still poorly understood. Here we studied DNA catenanes of bacterial plasmids arising as a result of DNA replication in Escherichia coli cells whose topoisomerase IV activity was inhibited. We combined high-resolution two-dimensional agarose gel electrophoresis with numerical simulations in order to better understand the relationship between the negative supercoiling of DNA generated by DNA gyrase and the DNA interlinking resulting from replication of circular DNA molecules. We showed that in those replication intermediates formed in vivo, catenation and negative supercoiling compete with each other. In interlinked molecules with high catenation numbers negative supercoiling is greatly limited. However, when interlinking decreases, as required for the segregation of newly replicated sister duplexes, their negative supercoiling increases. This observation indicates that negative supercoiling plays an active role during progressive decatenation of newly replicated DNA molecules in vivo
DNA supercoiling inhibits DNA knotting
Despite the fact that in living cells DNA molecules are long and highly crowded, they are rarely knotted. DNA knotting interferes with the normal functioning of the DNA and, therefore, molecular mechanisms evolved that maintain the knotting and catenation level below that which would be achieved if the DNA segments could pass randomly through each other. Biochemical experiments with torsionally relaxed DNA demonstrated earlier that type II DNA topoisomerases that permit inter- and intramolecular passages between segments of DNA molecules use the energy of ATP hydrolysis to select passages that lead to unknotting rather than to the formation of knots. Using numerical simulations, we identify here another mechanism by which topoisomerases can keep the knotting level low. We observe that DNA supercoiling, such as found in bacterial cells, creates a situation where intramolecular passages leading to knotting are opposed by the free-energy change connected to transitions from unknotted to knotted circular DNA molecules
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
“Breaking up is hard to do”: the formation and resolution of sister chromatid intertwines
The absolute necessity to resolve every intertwine between the two strands of the DNA double helix provides a massive challenge to the cellular processes that duplicate and segregate chromosomes. Although the overwhelming majority of intertwines between the parental DNA strands are resolved during DNA replication, there are numerous chromosomal contexts where some intertwining is maintained into mitosis. These mitotic sister chromatid intertwines (SCIs) can be found as; short regions of unreplicated DNA, fully replicated and intertwined sister chromatids—commonly referred to as DNA catenation—and as sister chromatid linkages generated by homologous recombination-associated processes. Several overlapping mechanisms, including intra-chromosomal compaction, topoisomerase action and Holliday junction resolvases, ensure that all SCIs are removed before they can prevent normal chromosome segregation. Here, I discuss why some DNA intertwines persist into mitosis and review our current knowledge of the SCI resolution mechanisms that are employed in both prokaryotes and eukaryotes, including how deregulating SCI formation during DNA replication or disrupting the resolution processes may contribute to aneuploidy in cancer
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