4,315 research outputs found
Size, shape, and flexibility of RNA structures
Determination of sizes and flexibilities of RNA molecules is important in
understanding the nature of packing in folded structures and in elucidating
interactions between RNA and DNA or proteins. Using the coordinates of the
structures of RNA in the Protein Data Bank we find that the size of the folded
RNA structures, measured using the radius of gyration, , follows the Flory
scaling law, namely, \AA where N is the number of
nucleotides. The shape of RNA molecules is characterized by the asphericity
and the shape parameters that are computed using the eigenvalues
of the moment of inertia tensor. From the distribution of , we find
that a large fraction of folded RNA structures are aspherical and the
distribution of values shows that RNA molecules are prolate (). The
flexibility of folded structures is characterized by the persistence length
. By fitting the distance distribution function to the worm-like
chain model we extracted the persistence length . We find that \AA. The dependence of on implies the average length of
helices should increases as the size of RNA grows. We also analyze packing in
the structures of ribosomes (30S, 50S, and 70S) in terms of , ,
, and . The 70S and the 50S subunits are more spherical compared to
most RNA molecules. The globularity in 50S is due to the presence of an
unusually large number (compared to 30S subunit) of small helices that are
stitched together by bulges and loops. Comparison of the shapes of the intact
70S ribosome and the constituent particles suggests that folding of the
individual molecules might occur prior to assembly.Comment: 28 pages, 8 figures, J. Chem. Phys. in pres
Stretching of a single-stranded DNA: Evidence for structural transition
Recent experiments have shown that the force-extension (F-x) curve for
single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is
significantly different from thymine [poly(dT)]. Here, we show that the base
stacking interaction is not sufficient to describe the F-x curves as seen in
the experiments. A reduction in the reaction co-ordinate arising from the
formation of helix at low forces and an increase in the distance between
consecutive phosphates of unstacked bases in the stretched state at high force
in the proposed model, qualitatively reproduces the experimentally observed
features. The multi-step plateau in the F-x curve is a signature of structural
change in ssDNA.Comment: 10 pages, 4 figure
Stretching an heteropolymer
We study the influence of some quenched disorder in the sequence of monomers
on the entropic elasticity of long polymeric chains. Starting from the
Kratky-Porod model, we show numerically that some randomness in the favoured
angles between successive segments induces a change in the elongation versus
force characteristics, and this change can be well described by a simple
renormalisation of the elastic constant. The effective coupling constant is
computed by an analytic study of the low force regime.Comment: Latex, 7 pages, 3 postscript figur
Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
We explore in detail the structural, mechanical and thermodynamic properties
of a coarse-grained model of DNA similar to that introduced in Thomas E.
Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101
(2010). Effective interactions are used to represent chain connectivity,
excluded volume, base stacking and hydrogen bonding, naturally reproducing a
range of DNA behaviour. We quantify the relation to experiment of the
thermodynamics of single-stranded stacking, duplex hybridization and hairpin
formation, as well as structural properties such as the persistence length of
single strands and duplexes, and the torsional and stretching stiffness of
double helices. We also explore the model's representation of more complex
motifs involving dangling ends, bulged bases and internal loops, and the effect
of stacking and fraying on the thermodynamics of the duplex formation
transition.Comment: 25 pages, 16 figure
The Yamabe invariant for axially symmetric two Kerr black holes initial data
An explicit 3-dimensional Riemannian metric is constructed which can be
interpreted as the (conformal) sum of two Kerr black holes with aligned angular
momentum. When the separation distance between them is large we prove that this
metric has positive Ricci scalar and hence positive Yamabe invariant. This
metric can be used to construct axially symmetric initial data for two Kerr
black holes with large angular momentum.Comment: 14 pages, 2 figure
Uniqueness and Non-uniqueness in the Einstein Constraints
The conformal thin sandwich (CTS) equations are a set of four of the Einstein
equations, which generalize the Laplace-Poisson equation of Newton's theory. We
examine numerically solutions of the CTS equations describing perturbed
Minkowski space, and find only one solution. However, we find {\em two}
distinct solutions, one even containing a black hole, when the lapse is
determined by a fifth elliptic equation through specification of the mean
curvature. While the relationship of the two systems and their solutions is a
fundamental property of general relativity, this fairly simple example of an
elliptic system with non-unique solutions is also of broader interest.Comment: 4 pages, 4 figures; abstract and introduction rewritte
Perturbative Solutions of the Extended Constraint Equations in General Relativity
The extended constraint equations arise as a special case of the conformal
constraint equations that are satisfied by an initial data hypersurface in
an asymptotically simple spacetime satisfying the vacuum conformal Einstein
equations developed by H. Friedrich. The extended constraint equations consist
of a quasi-linear system of partial differential equations for the induced
metric, the second fundamental form and two other tensorial quantities defined
on , and are equivalent to the usual constraint equations that satisfies
as a spacelike hypersurface in a spacetime satisfying Einstein's vacuum
equation. This article develops a method for finding perturbative,
asymptotically flat solutions of the extended constraint equations in a
neighbourhood of the flat solution on Euclidean space. This method is
fundamentally different from the `classical' method of Lichnerowicz and York
that is used to solve the usual constraint equations.Comment: This third and final version has been accepted for publication in
Communications in Mathematical Physic
A new geometric invariant on initial data for Einstein equations
For a given asymptotically flat initial data set for Einstein equations a new
geometric invariant is constructed. This invariant measure the departure of the
data set from the stationary regime, it vanishes if and only if the data is
stationary. In vacuum, it can be interpreted as a measure of the total amount
of radiation contained in the data.Comment: 5 pages. Important corrections regarding the generalization to the
non-time symmetric cas
High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Alternative splicing is a significant contributor to transcriptome diversity, and a high-throughput experimental method to quantitatively assess predictions from expressed sequence tag and microarray analyses may help to answer questions about the extent and functional significance of these variants. Here, we describe a method for high-throughput analysis of known or suspected alternative splicing variants (ASVs) using PCR, primer extension and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Reverse-transcribed mRNA is PCR amplified with primers surrounding the site of alternative splicing, followed by a primer extension reaction designed to target sequence disparities between two or more variants. These primer extension products are assayed on a MALDI-TOF mass spectrometer and analyzed automatically. This method is high-throughput, highly accurate and reproducible, allowing for the verification of the existence of splicing variants in a variety of samples. An example given also demonstrates how this method can eliminate potential pitfalls from ordinary gel electrophoretic analysis of splicing variants where heteroduplexes formed from different variants can produce erroneous results. The new method can be used to create alternative variant profiles for cancer markers, to study complex splicing regulation, or to screen potential splicing therapies
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