581,770 research outputs found
Bubble statistics and positioning in superhelically stressed DNA
We present a general framework to study the thermodynamic denaturation of
double-stranded DNA under superhelical stress. We report calculations of
position- and size-dependent opening probabilities for bubbles along the
sequence. Our results are obtained from transfer-matrix solutions of the
Zimm-Bragg model for unconstrained DNA and of a self-consistent linearization
of the Benham model for superhelical DNA. The numerical efficiency of our
method allows for the analysis of entire genomes and of random sequences of
corresponding length ( base pairs). We show that, at physiological
conditions, opening in superhelical DNA is strongly cooperative with average
bubble sizes of base pairs (bp), and orders of magnitude higher
than in unconstrained DNA. In heterogeneous sequences, the average degree of
base-pair opening is self-averaging, while bubble localization and statistics
are dominated by sequence disorder. Compared to random sequences with identical
GC-content, genomic DNA has a significantly increased probability to open large
bubbles under superhelical stress. These bubbles are frequently located
directly upstream of transcription start sites.Comment: to be appeared in Physical Review
Sequence sensitivity of breathing dynamics in heteropolymer DNA
We study the fluctuation dynamics of localized denaturation bubbles in
heteropolymer DNA with a master equation and complementary stochastic
simulation based on novel DNA stability data. A significant dependence of
opening probability and waiting time between bubble events on the local DNA
sequence is revealed and quantified for a biological sequence of the T7
bacteriophage. Quantitative agreement with data from fluorescence correlation
spectroscopy (FCS) is demonstrated.Comment: 4 pages, 5 figures, to appear in Physical Review Letter
Breathing dynamics in heteropolymer DNA
While the statistical mechanical description of DNA has a long tradition,
renewed interest in DNA melting from a physics perspective is nourished by
measurements of the fluctuation dynamics of local denaturation bubbles by
single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA
breathing) is supposedly crucial for biological functioning during, for
instance, transcription initiation and DNA's interaction with selectively
single-stranded DNA binding proteins. Motivated by this, we consider the bubble
breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master
equation and complementary stochastic Gillespie simulations, providing the
bubble size and the position of the bubble along the sequence as a function of
time. We utilize new experimental data that independently obtain stacking and
hydrogen bonding contributions to DNA stability. We calculate the spectrum of
relaxation times and the experimentally measurable autocorrelation function of
a fluorophore-quencher tagged base-pair, and demonstrate good agreement with
fluorescence correlation experiments. A significant dependence of opening
probability and waiting time between bubble events on the local DNA sequence is
revealed and quantified for a promoter sequence of the T7 phage. The strong
dependence on sequence, temperature and salt concentration for the breathing
dynamics of DNA found here points at a good potential for nanosensing
applications by utilizing short fluorophore-quencher dressed DNA constructs.Comment: 11 pages, 8 figure
Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
Understanding the melting of short DNA sequences probes DNA at the scale of
the genetic code and raises questions which are very different from those posed
by very long sequences, which have been extensively studied. We investigate
this problem by combining experiments and theory. A new experimental method
allows us to make a mapping of the opening of the guanines along the sequence
as a function of temperature. The results indicate that non-local effects may
be important in DNA because an AT-rich region is able to influence the opening
of a base pair which is about 10 base pairs away. An earlier mesoscopic model
of DNA is modified to correctly describe the time scales associated to the
opening of individual base pairs well below melting, and to properly take into
account the sequence. Using this model to analyze some characteristic sequences
for which detailed experimental data on the melting is available [Montrichok et
al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce
non-local effects of AT-rich regions to get acceptable results. This brings a
second indication that the influence of these highly fluctuating regions of DNA
on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte
Total syntheses of conformationally-locked difluorinated pentopyranose analogues and a pentopyranosyl phosphate mimetic
Trifluoroethanol has been elaborated, via a telescoped sequence involving a metalated difluoroenol, a difluoroallylic alcohol, [2,3]-Wittig rearrangement, and ultimately an RCM reaction and requiring minimal intermediate purification, to a number of cyclooctenone intermediates. Epoxidation of these intermediates followed by transannular ring opening or dihydroxylation, then transannular hemiacetalization delivers novel bicyclic analogues of pentopyranoses, which were elaborated (in one case) to an analogue of a glycosyl phosphate
Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case
The complementary strands of DNA molecules can be separated when stretched
apart by a force; the unzipping signal is correlated to the base content of the
sequence but is affected by thermal and instrumental noise. We consider here
the ideal case where opening events are known to a very good time resolution
(very large bandwidth), and study how the sequence can be reconstructed from
the unzipping data. Our approach relies on the use of statistical Bayesian
inference and of Viterbi decoding algorithm. Performances are studied
numerically on Monte Carlo generated data, and analytically. We show how
multiple unzippings of the same molecule may be exploited to improve the
quality of the prediction, and calculate analytically the number of required
unzippings as a function of the bandwidth, the sequence content, the elasticity
parameters of the unzipped strands
Field induced quantum-Hall ferromagnetism in suspended bilayer graphene
We have measured the magneto-resistance of freely suspended high-mobility
bilayer graphene. For magnetic fields T we observe the opening of a field
induced gap at the charge neutrality point characterized by a diverging
resistance. For higher fields the eight-fold degenerated lowest Landau level
lifts completely. Both the sequence of this symmetry breaking and the strong
transition of the gap-size point to a ferromagnetic nature of the insulating
phase developing at the charge neutrality point.Comment: 7 pages, 5 figure
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