1,050 research outputs found
How does the chromatin fiber deal with topological constraints?
In the nuclei of eukaryotic cells, DNA is packaged through several levels of
compaction in an orderly retrievable way that enables the correct regulation of
gene expression. The functional dynamics of this assembly involves the
unwinding of the so-called 30 nm chromatin fiber and accordingly imposes strong
topological constraints. We present a general method for computing both the
twist and the writhe of any winding pattern. An explicit derivation is
implemented for the chromatin fiber which provides the linking number of DNA in
eukaryotic chromosomes. We show that there exists one and only one unwinding
path which satisfies both topological and mechanical constraints that DNA has
to deal with during condensation/decondensation processes.Comment: Presented in Nature "News and views in brief" Vol. 429 (13 May 2004).
Movies available at
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Multi-site H-bridge breathers in a DNA--shaped double strand
We investigate the formation process of nonlinear vibrational modes
representing broad H-bridge multi--site breathers in a DNA--shaped double
strand.
Within a network model of the double helix we take individual motions of the
bases within the base pair plane into account. The resulting H-bridge
deformations may be asymmetric with respect to the helix axis. Furthermore the
covalent bonds may be deformed distinctly in the two backbone strands.
Unlike other authors that add different extra terms we limit the interaction
to the hydrogen bonds within each base pair and the covalent bonds along each
strand. In this way we intend to make apparent the effect of the characteristic
helicoidal structure of DNA. We study the energy exchange processes related
with the relaxation dynamics from a non-equilibrium conformation. It is
demonstrated that the twist-opening relaxation dynamics of a radially distorted
double helix attains an equilibrium regime characterized by a multi-site
H-bridge breather.Comment: 27 pages and 10 figure
Base sequence dependent sliding of proteins on DNA
The possibility that the sliding motion of proteins on DNA is influenced by
the base sequence through a base pair reading interaction, is considered.
Referring to the case of the T7 RNA-polymerase, we show that the protein should
follow a noise-influenced sequence-dependent motion which deviate from the
standard random walk usually assumed. The general validity and the implications
of the results are discussed.Comment: 12 pages, 3 figure
Solitons in Yakushevich-like models of DNA dynamics with improved intrapair potential
The Yakushevich (Y) model provides a very simple pictures of DNA torsion
dynamics, yet yields remarkably correct predictions on certain physical
characteristics of the dynamics. In the standard Y model, the interaction
between bases of a pair is modelled by a harmonic potential, which becomes
anharmonic when described in terms of the rotation angles; here we substitute
to this different types of improved potentials, providing a more physical
description of the H-bond mediated interactions between the bases. We focus in
particular on soliton solutions; the Y model predicts the correct size of the
nonlinear excitations supposed to model the ``transcription bubbles'', and this
is essentially unchanged with the improved potential. Other features of soliton
dynamics, in particular curvature of soliton field configurations and the
Peierls-Nabarro barrier, are instead significantly changed
Breathers in a system with helicity and dipole interaction
Recent papers that have studied variants of the Peyrard-Bishop model for DNA,
have taken into account the long range interaction due to the dipole moments of
the hydrogen bonds between base pairs. In these models the helicity of the
double strand is not considered. In this particular paper we have performed an
analysis of the influence of the helicity on the properties of static and
moving breathers in a Klein--Gordon chain with dipole-dipole interaction. It
has been found that the helicity enlarges the range of existence and stability
of static breathers, although this effect is small for a typical helical
structure of DNA. However the effect of the orientation of the dipole moments
is considerably higher with transcendental consequences for the existence of
mobile breathers.Comment: 4pages, 5 eps figure
Human Cytomegalovirus: detection of congenital and perinatal infection in Argentina
BACKGROUND: Human cytomegalovirus (CMV) is one of the most commonly found agents of congenital infections. Primary maternal infection is associated with risk of symptomatic congenital diseases, and high morbidity is frequently associated with very low birth weight. Neonates with asymptomatic infection develop various sequelae during infancy. This is the first Argentine study performed in neonates with congenital and postnatal HCMV infection. The purpose of this study was to evaluate the performance of the polymerase chain reaction (PCR) technique with different pairs of primers, to detect cytomegalovirus isolated in tissue cultures and directly in urine and dried blood spot (DBS) specimens. Results were compared with IgM detection. METHODS: The study was performed between 1999 and 2001 on routine samples in the Laboratory. A total of 61 urine and 56 serum samples were selected from 61 newborns/infants, 33 patients whose samples were analyzed during the first two to three weeks of life were considered congenital infections; the remaining 28 patients whose samples were taken later than the third week were grouped as perinatal infections, although only in 4 the perinatal transmission of infection was determined unequivocally Cytomegalovirus diagnosis was made by isolating the virus from urine samples in human foreskin fibroblast cells. Three different primer pairs directed to IE, LA and gB genes were used for the HCMV PCR assay in viral isolates. Subsequently, PCR and nested PCR (nPCR) assays with gB primers were performed directly in urine and in 11 samples of dried blood spot (DBS) on Guthrie Card, these results were then compared with serology. RESULTS: The main clinical manifestations of the 33 patients with congenital infection were purpura, jaundice, hepatomegaly and anaemia. Three patients presented low birth weight as single symptom, 10, intracranial calcifications, and 2, kidney failure. In the 28 patients grouped as with perinatal infection, anaemia, hepatosplenomegaly and enzymatic alteration were predominant, and 4 patients were HIV positive. The primers used to amplify the gB region had a PCR positivity rate of 100%, whereas those that amplified IE and LA regions had a PCR positivity rate of 54% and 61% respectively, in CMV isolates. Amplification by PCR of urine samples (with no previous DNA extraction), using primers for the gB region, detected 34/61 positive samples. Out of the 33 samples from patients with congenital infection, 24 (73%) were positive. When nPCR was used in these samples, all were positive, whereas in the remaining 28 patients, two negative cases were found. Cytomegalovirus DNA detection in 11 samples was also carried out in DBS: 7 DBS samples were positive and 4 were negative. CONCLUSIONS: Primers directed to the gB fragment region were the best choice for the detection of CMV DNA in positive isolates. In congenital infections, direct PCR in urine was positive in a high percentage (73%) of samples; however, in patients grouped as with perinatal infection only 36% of the cases were positive. With n-PCR, total sample positivity reached 97%. PCR technique performed in DBS allowed identifying congenital infection in four patients and to be confirmed in 3. These results show the value of nPCR for the detection of all cases of CMV infection. The assay offers the advantage that it may be performed within the normal working day and provides reliable results in a much shorter time frame than that required for either traditional tissue culture or the shell-viral assay
Energy funneling in a bent chain of Morse oscillators with long-range coupling
A bent chain of coupled Morse oscillators with long-range dispersive
interaction is considered. Moving localized excitations may be trapped in the
bending region. Thus chain geometry acts like an impurity. An energy funneling
effect is observed in the case of random initial conditions.Comment: 6 pages, 12 figures. Submitted to Physical Review E, Oct. 13, 200
Statistical Mechanics of Torque Induced Denaturation of DNA
A unifying theory of the denaturation transition of DNA, driven by
temperature T or induced by an external mechanical torque Gamma is presented.
Our model couples the hydrogen-bond opening and the untwisting of the
helicoidal molecular structure. We show that denaturation corresponds to a
first-order phase transition from B-DNA to d-DNA phases and that the
coexistence region is naturally parametrized by the degree of supercoiling
sigma. The denaturation free energy, the temperature dependence of the twist
angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma
plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve
Dynamical model for DNA sequences
This article discusses a dynamical model for DNA sequences based on the assumption that the statistical properties of DNA paths are determined by the joint action of two processes, one deterministic with long-range correlations and the other random and δ-function correlated
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