827 research outputs found
Effective charge and free energy of DNA inside an ion channel
Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin
channel in a lipid membrane driven by applied transmembrane voltage V was
extensively studied recently. While the bare charge of the ssDNA piece inside
the channel is approximately 12 (in units of electron charge) measurements of
different effective charges resulted in values between one and two. We explain
these challenging observations by a large self-energy of a charge in the narrow
water filled gap between ssDNA and channel walls, related to large difference
between dielectric constants of water and lipid, and calculate effective
charges of ssDNA. We start from the most fundamental stall charge , which
determines the force stalling DNA against the voltage V (L is
the length of the channel). We show that the stall charge is proportional
to the ion current blocked by DNA, which is small due to the self-energy
barrier. Large voltage V reduces the capture barrier which DNA molecule should
overcome in order to enter the channel by , where is the
effective capture charge. We expressed it through the stall charge . We
also relate the stall charge to two other effective charges measured for
ssDNA with a hairpin in the back end: the charge responsible for
reduction of the barrier for unzipping of the hairpin and the charge
responsible for DNA escape in the direction of hairpin against the voltage. At
small V we explain reduction of the capture barrier with the salt
concentration.Comment: Typos are correcte
Self-energy limited ion transport in sub-nanometer channels
The current-voltage characteristics of the alpha-Hemolysin protein pore
during the passage of single-stranded DNA under varying ionic strength, C, are
studied experimentally. We observe strong blockage of the current, weak
super-linear growth of the current as a function of voltage, and a minimum of
the current as a function of C. These observations are interpreted as the
result of the ion electrostatic self-energy barrier originating from the large
difference in the dielectric constants of water and the lipid bilayer. The
dependence of DNA capture rate on C also agrees with our model.Comment: more experimental material is added. 4 pages, 7 figure
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
Reversible Metal-Semiconductor Transition of ssDNA-Decorated Single-Walled Carbon Nanotubes
A field effect transistor (FET) measurement of a SWNT shows a transition from
a metallic one to a p-type semiconductor after helical wrapping of DNA. Water
is found to be critical to activate this metal-semiconductor transition in the
SWNT-ssDNA hybrid. Raman spectroscopy confirms the same change in electrical
behavior. According to our ab initio calculations, a band gap can open up in a
metallic SWNT with wrapped ssDNA in the presence of water molecules due to
charge transfer.Comment: 13 pages, 6 figure
Numerical Calculations of the B1g Raman Spectrum of the Two-Dimensional Heisenberg Model
The B1g Raman spectrum of the two-dimensional S=1/2 Heisenberg model is
discussed within Loudon-Fleury theory at both zero and finite temperature. The
exact T=0 spectrum for lattices with up to 6*6 sites is computed using Lanczos
exact diagonalization. A quantum Monte Carlo (QMC) method is used to calculate
the corresponding imaginary-time correlation function and its first two
derivatives for lattices with up to 16*16 spins. The imaginary-time data is
continued to real frequency using the maximum-entropy method, as well as a fit
based on spinwave theory. The numerical results are compared with spinwave
calculations for finite lattices. There is a surprisingly large change in the
exact spectrum going from 4*4 to 6*6 sites. In the former case there is a
single dominant two-magnon peak at frequency w/J appr. 3.0, whereas in the
latter case there are two approximately equal-sized peaks at w/J appr. 2.7 and
3.9. This is in good qualitative agreement with the spinwave calculations
including two-magnon processes on the same lattices. Both the Lanczos and the
QMC results indicate that the actual infinite-size two-magnon profile is
broader than the narrow peak obtained in spinwave theory, but the positions of
the maxima agree to within a few percent. The higher-order contributions
present in the numerical results are merged with the two-magnon profile and
extend up to frequencies w/J appr. 7. The first three frequency cumulants of
the spectrum are in excellent agreement with results previously obtained from a
series expansion around the Ising limit. Typical experimental B1g$ spectra for
La2CuO4 are only slightly broader than what we obtain here. The exchange
constant extracted from the peak position is J appr. 1400K, in good agreement
with values obtained from neutron scattering and NMR experiments.Comment: 15 pages, Revtex, 13 PostScript figure
Chromatin: a tunable spring at work inside chromosomes
This paper focuses on mechanical aspects of chromatin biological functioning.
Within a basic geometric modeling of the chromatin assembly, we give for the
first time the complete set of elastic constants (twist and bend persistence
lengths, stretch modulus and twist-stretch coupling constant) of the so-called
30-nm chromatin fiber, in terms of DNA elastic properties and geometric
properties of the fiber assembly. The computation naturally embeds the fiber
within a current analytical model known as the ``extensible worm-like rope'',
allowing a straightforward prediction of the force-extension curves. We show
that these elastic constants are strongly sensitive to the linker length, up to
1 bp, or equivalently to its twist, and might locally reach very low values,
yielding a highly flexible and extensible domain in the fiber. In particular,
the twist-stretch coupling constant, reflecting the chirality of the chromatin
fiber, exhibits steep variations and sign changes when the linker length is
varied.
We argue that this tunable elasticity might be a key feature for chromatin
function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure
Attraction between DNA molecules mediated by multivalent ions
The effective force between two parallel DNA molecules is calculated as a
function of their mutual separation for different valencies of counter- and
salt ions and different salt concentrations. Computer simulations of the
primitive model are used and the shape of the DNA molecules is accurately
modelled using different geometrical shapes. We find that multivalent ions
induce a significant attraction between the DNA molecules whose strength can be
tuned by the averaged valency of the ions. The physical origin of the
attraction is traced back either to electrostatics or to entropic
contributions. For multivalent counter- and monovalent salt ions, we find a
salt-induced stabilization effect: the force is first attractive but gets
repulsive for increasing salt concentration. Furthermore, we show that the
multivalent-ion-induced attraction does not necessarily correlate with DNA
overcharging.Comment: 51 pages and 13 figure
Wringing out DNA
The chiral nature of DNA plays a crucial role in cellular processes. Here we
use magnetic tweezers to explore one of the signatures of this chirality, the
coupling between stretch and twist deformations. We show that the extension of
a stretched DNA molecule increases linearly by 0.42 nm per excess turn applied
to the double helix. This result contradicts the intuition that DNA should
lengthen as it is unwound and get shorter with overwinding. We then present
numerical results of energy minimizations of torsionally restrained DNA that
display a behaviour similar to the experimental data and shed light on the
molecular details of this surprising effect.Comment: 4 pages revtex4, 4 figure
Merging late Holocene molecular organic and foraminiferal-based geochemical records of sea surface temperature in the Gulf of Mexico
Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 26 (2011): PA1209, doi:10.1029/2010PA002000.A molecular organic geochemical proxy (TEX86) for sea surface temperature (SST) is compared with a foraminifera-based SST proxy (Mg/Ca) in a decadal-resolution marine sedimentary record spanning the last 1000 years from the Gulf of Mexico. We assess the relative strengths of the organic and inorganic paleoceanographic techniques for reconstructing high-resolution SST variability during recent climate events, including the Little Ice Age (LIA) and the Medieval Warm Period (MWP). SST estimates based on the molecular organic proxy TEX86 show a similar magnitude and pattern of SST variability to foraminiferal Mg/Ca-SST estimates but with some important differences. For instance, both proxies show a cooling (1°C–2°C) of Gulf of Mexico SSTs during the LIA. During the MWP, however, Mg/Ca-SSTs are similar to near-modern SSTs, while TEX86 indicates SSTs that were cooler than modern. Using the respective SST calibrations for each proxy results in TEX86-SST estimates that are 2°C–4°C warmer than Mg/Ca-SST throughout the 1000 year record. We interpret the TEX86-SST as a summer-weighted SST signal from the upper mixed layer, whereas the Mg/Ca-SST better reflects the mean annual SST. Downcore differences in the SST estimates between the two proxies (ΔT = TEX86 − Mg/Ca) are interpreted in the context of varying seasonality and/or changing water column temperature gradients.This work was supported,
in part, by the National Science Foundation under grants OCE‐0318361
and OCE‐0903017
Studying Early Lethality of 45,XO (Turner's Syndrome) Embryos Using Human Embryonic Stem Cells
Turner's syndrome (caused by monosomy of chromosome X) is one of the most common chromosomal abnormalities in females. Although 3% of all pregnancies start with XO embryos, 99% of these pregnancies terminate spontaneously during the first trimester. The common genetic explanation for the early lethality of monosomy X embryos, as well as the phenotype of surviving individuals is haploinsufficiency of pseudoautosomal genes on the X chromosome. Another possible mechanism is null expression of imprinted genes on the X chromosome due to the loss of the expressed allele. In contrast to humans, XO mice are viable, and fertile. Thus, neither cells from patients nor mouse models can be used in order to study the cause of early lethality in XO embryos. Human embryonic stem cells (HESCs) can differentiate in culture into cells from the three embryonic germ layers as well as into extraembryonic cells. These cells have been shown to have great value in modeling human developmental genetic disorders. In order to study the reasons for the early lethality of 45,XO embryos we have isolated HESCs that have spontaneously lost one of their sex chromosomes. To examine the possibility that imprinted genes on the X chromosome play a role in the phenotype of XO embryos, we have identified genes that were no longer expressed in the mutant cells. None of these genes showed a monoallelic expression in XX cells, implying that imprinting is not playing a major role in the phenotype of XO embryos. To suggest an explanation for the embryonic lethality caused by monosomy X, we have differentiated the XO HESCs in vitro an in vivo. DNA microarray analysis of the differentiated cells enabled us to compare the expression of tissue specific genes in XO and XX cells. The tissue that showed the most significant differences between the clones was the placenta. Many placental genes are expressed at much higher levels in XX cells in compare to XO cells. Thus, we suggest that abnormal placental differentiation as a result of haploinsufficiency of X-linked pseudoautosomal genes causes the early lethality in XO human embryos
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