3,468 research outputs found
Dynamics of a bubble formed in double stranded DNA
We study the fluctuational dynamics of a tagged base-pair in double stranded
DNA. We calculate the drift force which acts on the tagged base-pair using a
potential model that describes interactions at base pairs level and use it to
construct a Fokker-Planck equation.The calculated displacement autocorrelation
function is found to be in very good agreement with the experimental result of
Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the
entire time range of measurement. We calculate the most probable displacements
which predominately contribute to the autocorrelation function and the
half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let
DNA bubble dynamics as a quantum Coulomb problem
We study the dynamics of denaturation bubbles in double-stranded DNA on the
basis of the Poland-Scheraga model. We demonstrate that the associated
Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting
temperature the bubble lifetime is associated with the continuum of scattering
states of the repulsive Coulomb potential, at the melting temperature the
Coulomb potential vanishes and the underlying first exit dynamics exhibits a
long time power law tail, above the melting temperature, corresponding to an
attractive Coulomb potential, the long time dynamics is controlled by the
lowest bound state. Correlations and finite size effects are discussed.Comment: 4 pages, 3 figures, revte
Two-Dimensional Crystallography of TFIIB– and IIE–RNA Polymerase II Complexes: Implications for Start Site Selection and Initiation Complex Formation
AbstractTranscription factors IIB (TFIIB) and IIE (TFIIE) bound to RNA polymerase II have been revealed by electron crystallography in projection at 15.7 Å resolution. The results lead to simple hypotheses for the roles of these factors in the initiation of transcription. TFIIB is suggested to define the distance from TATA box to transcription start site by bringing TATA DNA in contact with polymerase at that distance from the active center of the enzyme. TFIIE is suggested to participate in a key conformational switch occurring at the active center upon polymerase–DNA interaction
Dynamics of DNA-breathing: Weak noise analysis, finite time singularity, and mapping onto the quantum Coulomb problem
We study the dynamics of denaturation bubbles in double-stranded DNA on the
basis of the Poland-Scheraga model. We show that long time distributions for
the survival of DNA bubbles and the size autocorrelation function can be
derived from an asymptotic weak noise approach. In particular, below the
melting temperature the bubble closure corresponds to a noisy finite time
singularity. We demonstrate that the associated Fokker-Planck equation is
equivalent to a quantum Coulomb problem. Below the melting temperature the
bubble lifetime is associated with the continuum of scattering states of the
repulsive Coulomb potential; at the melting temperature the Coulomb potential
vanishes and the underlying first exit dynamics exhibits a long time power law
tail; above the melting temperature, corresponding to an attractive Coulomb
potential, the long time dynamics is controlled by the lowest bound state.
Correlations and finite size effects are discussed.Comment: 12 pages, 10 figures, revte
Pulling a polymer out of a potential well and the mechanical unzipping of DNA
Motivated by the experiments on DNA under torsion, we consider the problem of
pulling a polymer out of a potential well by a force applied to one of its
ends. If the force is less than a critical value, then the process is activated
and has an activation energy proportinal to the length of the chain. Above this
critical value, the process is barrierless and will occur spontaneously. We use
the Rouse model for the description of the dynamics of the peeling out and
study the average behaviour of the chain, by replacing the random noise by its
mean. The resultant mean-field equation is a nonlinear diffusion equation and
hence rather difficult to analyze. We use physical arguments to convert this in
to a moving boundary value problem, which can then be solved exactly. The
result is that the time required to pull out a polymer of segments
scales like . For models other than the Rouse, we argue that Comment: 11 pages, 6 figures. To appear in PhysicalReview
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
Increased Expression of Tissue Factor and Receptor for Advanced Glycation End Products in Peripheral Blood Mononuclear Cells of Patients With Type 2 Diabetes Mellitus with Vascular Complications
The aim of the study was to determine the correlation between
the expression of tissue factor (TF) and the receptor
for advanced glycation end products (RAGEs) and vascular
complications in patients with longstanding uncontrolled
type 2 diabetes (T2D). TF and RAGE mRNAs as well as
TF antigen and activity were investigated in 21 T2D patients
with and without vascular complications. mRNA expression
was assessed by reverse transcriptase–polymerase
chain reaction (RT-PCR) in nonstimulated and advanced
glycation end product (AGE) albumin–stimulated peripheral
blood mononuclear cells (PBMCs). TF antigen expression
was determined by enzyme-linked immunosorbent assay
(ELISA) and TF activity by a modified prothrombin
time assay. Basal RAGE mRNA expression was 0.2 ± 0.06
in patients with complications and 0.05 ± 0.06 patients without
complications (P = .004). Stimulation did not cause any
further increase in either group. TF mRNA was 0.58 ± 0.29
in patients with complications and 0.21 ± 0.18 in patients
without complications (P = .003). Stimulation resulted in
a nonsignificant increase in both groups. Basal TF activity
(U/106 PBMCs) was 18.4 ± 13.2 in patients with complications
and 6.96 ± 5.2 in patients without complications (P =
.003). It increased 3-fold in both groups after stimulation
(P = .001). TF antigen (pg/106 PBMCs) was 33.7 ± 28.6 in
patients with complications, 10.4 ± 7.8 in patients without complications (P = .02). Stimulation tripled TF antigen in
both groups of patients (P = .001). The RAGE/TF axis is
up-regulated inT2Dpatients with vascular complications as
compared to patients without complications. This suggests
a role for this axis in the pathogenesis of vascular complications
in T2D
Master equation approach to DNA-breathing in heteropolymer DNA
After crossing an initial barrier to break the first base-pair (bp) in
double-stranded DNA, the disruption of further bps is characterized by free
energies between less than one to a few kT. This causes the opening of
intermittent single-stranded bubbles. Their unzipping and zipping dynamics can
be monitored by single molecule fluorescence or NMR methods. We here establish
a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of
a master equation that governs the time evolution of the joint probability
distribution for the bubble size and position along the sequence. The transfer
coefficients are based on the Poland-Scheraga free energy model. We derive the
autocorrelation function for the bubble dynamics and the associated relaxation
time spectrum. In particular, we show how one can obtain the probability
densities of individual bubble lifetimes and of the waiting times between
successive bubble events from the master equation. A comparison to results of a
stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure
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