2,071 research outputs found
Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
We investigate the coalescence of two DNA-bubbles initially located at weak
segments and separated by a more stable barrier region in a designed construct
of double-stranded DNA. The characteristic time for bubble coalescence and the
corresponding distribution are derived, as well as the distribution of
coalescence positions along the barrier. Below the melting temperature, we find
a Kramers-type barrier crossing behaviour, while at high temperatures, the
bubble corners perform drift-diffusion towards coalescence. The results are
obtained by mapping the bubble dynamics on the problem of two vicious walkers
in opposite potentials.Comment: 7 pages, 4 figure
Dynamical scaling of the DNA unzipping transition
We report studies of the equilibrium and the dynamics of a general set of
lattice models which capture the essence of the force-induced or mechanical DNA
unzipping transition. Besides yielding the whole equilibrium phase diagram in
the force vs temperature plane, which reveals the presence of an interesting
re-entrant unzipping transition for low T, these models enable us to
characterize the dynamics of the process starting from a non-equilibrium
initial condition. The thermal melting of the DNA strands displays a model
dependent time evolution. On the contrary, our results suggest that the
dynamical mechanism for the unzipping by force is very robust and the scaling
behaviour does not depend on the details of the description we adopt.Comment: 6 pages, 4 figures, A shorter version of this paper appeared in Phys.
Rev. Lett. 88, 028102 (2002
Denaturation transition of stretched DNA
We generalize the Poland-Scheraga model to consider DNA denaturation in the
presence of an external stretching force. We demonstrate the existence of a
force-induced DNA denaturation transition and obtain the temperature-force
phase diagram. The transition is determined by the loop exponent for which
we find the new value such that the transition is second order
with in . We show that a finite stretching force
destabilizes DNA, corresponding to a lower melting temperature , in
agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites
The positions of nucleosomes in eukaryotic genomes determine which parts of
the DNA sequence are readily accessible for regulatory proteins and which are
not. Genome-wide maps of nucleosome positions have revealed a salient pattern
around transcription start sites, involving a nucleosome-free region (NFR)
flanked by a pronounced periodic pattern in the average nucleosome density.
While the periodic pattern clearly reflects well-positioned nucleosomes, the
positioning mechanism is less clear. A recent experimental study by Mavrich et
al. argued that the pattern observed in S. cerevisiae is qualitatively
consistent with a `barrier nucleosome model', in which the oscillatory pattern
is created by the statistical positioning mechanism of Kornberg and Stryer. On
the other hand, there is clear evidence for intrinsic sequence preferences of
nucleosomes, and it is unclear to what extent these sequence preferences affect
the observed pattern. To test the barrier nucleosome model, we quantitatively
analyze yeast nucleosome positioning data both up- and downstream from NFRs.
Our analysis is based on the Tonks model of statistical physics which
quantifies the interplay between the excluded-volume interaction of nucleosomes
and their positional entropy. We find that although the typical patterns on the
two sides of the NFR are different, they are both quantitatively described by
the same physical model, with the same parameters, but different boundary
conditions. The inferred boundary conditions suggest that the first nucleosome
downstream from the NFR (the +1 nucleosome) is typically directly positioned
while the first nucleosome upstream is statistically positioned via a
nucleosome-repelling DNA region. These boundary conditions, which can be
locally encoded into the genome sequence, significantly shape the statistical
distribution of nucleosomes over a range of up to ~1000 bp to each side.Comment: includes supporting materia
Polymer reptation and nucleosome repositioning
We consider how beads can diffuse along a chain that wraps them, without
becoming displaced from the chain; our proposed mechanism is analogous to the
reptation of "stored length" in more familiar situations of polymer dynamics.
The problem arises in the case of globular aggregates of proteins (histones)
that are wound by DNA in the chromosomes of plants and animals; these beads
(nucleosomes) are multiply wrapped and yet are able to reposition themselves
over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let
Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
We investigate the coalescence of two DNA-bubbles initially located at weak
domains and separated by a more stable barrier region in a designed construct
of double-stranded DNA. In a continuum Fokker-Planck approach, the
characteristic time for bubble coalescence and the corresponding distribution
are derived, as well as the distribution of coalescence positions along the
barrier. Below the melting temperature, we find a Kramers-type barrier crossing
behavior, while at high temperatures, the bubble corners perform
drift-diffusion towards coalescence. In the calculations, we map the bubble
dynamics on the problem of two vicious walkers in opposite potentials. We also
present a discrete master equation approach to the bubble coalescence problem.
Numerical evaluation and stochastic simulation of the master equation show
excellent agreement with the results from the continuum approach. Given that
the coalesced state is thermodynamically stabilized against a state where only
one or a few base pairs of the barrier region are re-established, it appears
likely that this type of setup could be useful for the quantitative
investigation of thermodynamic DNA stability data as well as the rate constants
involved in the unzipping and zipping dynamics of DNA, in single molecule
fluorescence experiments.Comment: 24 pages, 11 figures; substantially extended version of
cond-mat/0610752; v2: minor text changes, virtually identical to the
published versio
Polyhedral vesicles
Polyhedral vesicles with a large bending modulus of the membrane such as the
gel phase lipid membrane were studied using a Brownian dynamics simulation. The
vesicles exhibit various polyhedral morphologies such as tetrahedron and cube
shapes. We clarified two types of line defects on the edges of the polyhedrons:
cracks of both monolayers at the spontaneous curvature of monolayer , and a crack of the inner monolayer at . Around the
latter defect, the inner monolayer curves positively. Our results suggested
that the polyhedral morphology is controlled by .Comment: 4 pages, 5 figure
The antimicrobial polymer PHMB enters cells and selectively condenses bacterial chromosomes
To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance
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