105 research outputs found
Comment on "Bubble nucleation and cooperativity in DNA melting" [Phys. Rev. Letters 94, 035504 (2005), arXiv:cond-mat/0412591]
The conclusions presented in this Letter arXiv:cond-mat/0412591 rely on not
converged calculations and should be considered with caution.Comment: accepted as a "Comment" in PR
Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling
International audienceRunning title: DNA demixing and supercoiling. Abstract: This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this paper, we investigate the interplay of these two mechanisms, with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime where the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold, as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixin
Towards more realistic dynamical models for DNA secondary structure
We propose a dynamical model for the secondary structure of DNA, which is
based on the finite stacking enthalpies used in thermodynamics calculations. In
this model, the two strands can separate and the bases are allowed to rotate
perpendicular to the sequence axis. We show, through molecular dynamics
simulations, that the model has the correct behaviour at the denaturation
transition.Comment: accepted for publication in Chemical Physics Letter
Organization of the bacterial nucleoid by DNA-bridging proteins and globular crowders
The genomic DNA of bacteria occupies only a fraction of the cell called the
nucleoid, although it is not bounded by any membrane and would occupy a volume
hundreds of times larger than the cell in the absence of constraints. The two
most important contributions to the compaction of the DNA coil are the
cross-linking of the DNA by nucleoid proteins (like H-NS and StpA) and the
demixing of DNA and other abundant globular macromolecules which do not bind to
the DNA (like ribosomes). The present work deals with the interplay of
DNA-bridging proteins and globular macromolecular crowders, with the goal of
determining the extent to which they collaborate in organizing the nucleoid. In
order to answer this question, a coarse-grained model was developed and its
properties were investigated through Brownian dynamics simulations. These
simulations reveal that the radius of gyration of the DNA coil decreases
linearly with the effective volume ratio of globular crowders and the number of
DNA bridges formed by nucleoid proteins in the whole range of physiological
values. Moreover, simulations highlight the fact that the number of DNA bridges
formed by nucleoid proteins depends crucially on their ability to
self-associate (oligomerize). An explanation for this result is proposed in
terms of the mean distance between DNA segments and the capacity of proteins to
maintain DNA--bridging in spite of the thermal fluctuations of the DNA network.
Finally, simulations indicate that non-associating proteins preserve a high
mobility inside the nucleoid while contributing to its compaction, leading to a
DNA/protein complex which looks like a liquid droplet. In contrast,
self-associating proteins form a little deformable network which cross-links
the DNA chain, with the consequence that the DNA/protein complex looks more
like a gel
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