519 research outputs found
Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers
that condense into a compact structure. We use optical tweezers to pull
condensed fibers and investigate the decondensation transition by measuring
force-extension curves (FECs). A characteristic plateau force (around 10 pN)
and hysteresis between the pulling and relaxation cycles are observed for
different dendrimer sizes, indicating the existence of a first-order transition
between two phases (condensed and extended) of the fiber. The fact that we can
reproduce the same FECs in the absence of additional dendrimers in the buffer
medium indicates that dendrimers remain irreversibly bound to the DNA backbone.
Upon salt variation FECs change noticeably confirming that electrostatic forces
drive the condensation transition. Finally, we propose a simple model for the
decondensing transition that qualitatively reproduces the FECs and which is
confirmed by AFM images.Comment: Latex version, 4 pages+3 color figure
A one-dimensional model for theoretical analysis of single molecule experiments
In this paper we compare two polymer stretching experiments. The outcome of
both experiments is a force-extension relation. We use a one-dimensional model
to show that in general the two quantities are not equal. In certain limits,
however, both force-extension relations coincide.Comment: 11 pages, 5 figure
Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes
We investigate the thermodynamics and kinetics of DNA hairpins that
fold/unfold under the action of applied mechanical force. We introduce the
concept of the molecular free energy landscape and derive simplified
expressions for the force dependent Kramers-Bell rates. To test the theory we
have designed a specific DNA hairpin sequence that shows two-state cooperative
folding under mechanical tension and carried out pulling experiments using
optical tweezers. We show how we can determine the parameters that characterize
the molecular free energy landscape of such sequence from rupture force kinetic
studies. Finally we combine such kinetic studies with experimental
investigations of the Crooks fluctuation relation to derive the free energy of
formation of the hairpin at zero force.Comment: 28 pages, 12 figure
Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation
We investigate irreversibility and dissipation in single molecules that
cooperatively fold/unfold in a two state manner under the action of mechanical
force. We apply path thermodynamics to derive analytical expressions for the
average dissipated work and the average hopping number in two state systems. It
is shown how these quantities only depend on two parameters that characterize
the folding/unfolding kinetics of the molecule: the fragility and the
coexistence hopping rate. The latter has to be rescaled to take into account
the appropriate experimental setup. Finally we carry out pulling experiments
with optical tweezers in a specifically designed DNA hairpin that shows
two-state cooperative folding. We then use these experimental results to
validate our theoretical predictions.Comment: 28 pages, 12 figure
A two-parameter random walk with approximate exponential probability distribution
We study a non-Markovian random walk in dimension 1. It depends on two
parameters eps_r and eps_l, the probabilities to go straight on when walking to
the right, respectively to the left. The position x of the walk after n steps
and the number of reversals of direction k are used to estimate eps_r and
eps_l. We calculate the joint probability distribution p_n(x,k) in closed form
and show that, approximately, it belongs to the exponential family.Comment: 12 pages, updated reference to companion paper cond-mat/060126
Elasticity model of a supercoiled DNA molecule
Within a simple elastic theory, we study the elongation versus force
characteristics of a supercoiled DNA molecule at thermal equilibrium in the
regime of small supercoiling. The partition function is mapped to the path
integral representation for a quantum charged particle in the field of a
magnetic monopole with unquantized charge.
We show that the theory is singular in the continuum limit and must be
regularised at an intermediate length scale. We find good agreement with
existing experimental data, and point out how to measure the twist rigidity
accurately.Comment: Latex, 4 pages. The figure contains new experimental data, giving a
new determination of the twist rigidit
Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA
By resorting to the thick-chain model we discuss how the stretching response
of a polymer is influenced by the self-avoidance entailed by its finite
thickness. The characterization of the force versus extension curve for a thick
chain is carried out through extensive stochastic simulations. The
computational results are captured by an analytic expression that is used to
fit experimental stretching measurements carried out on DNA and single-stranded
RNA (poly-U) in various solutions. This strategy allows us to infer the
apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and
poly-U, for different ionic strengths. Due to the very different degree of
flexibility of the two molecules, the results provide insight into how the
apparent diameter is influenced by the interplay between the
(solution-dependent) Debye screening length and the polymers' ``bare''
thickness. For DNA, the electrostatic contribution to the effective radius,
, is found to be about 5 times larger than the Debye screening length,
consistently with previous theoretical predictions for highly-charged stiff
rods. For the more flexible poly-U chains the electrostatic contribution to
is found to be significantly smaller than the Debye screening length.Comment: iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matte
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
Theory of biopolymer stretching at high forces
We provide a unified theory for the high force elasticity of biopolymers
solely in terms of the persistence length, , and the monomer spacing,
. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely
Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the
Worm-like Chain (WLC) is a better model. We show that can be estimated
from the force extension curve (FEC) at the extension
(normalized by the contour length of the biopolymer). After validating the
theory using simulations, we provide a quantitative analysis of the FECs for a
diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and
unstructured PEVK domain of titin) for . The success of a specific
polymer model (FJC or WLC) to describe the FEC of a given biopolymer is
naturally explained by the theory. Only by probing the response of biopolymers
over a wide range of forces can the -dependent elasticity be fully
described.Comment: 20 pages, 4 figure
Single-molecule derivation of salt dependent base-pair free energies in DNA
Accurate knowledge of the thermodynamic properties of nucleic acids is
crucial to predicting their structure and stability. To date most measurements
of base-pair free energies in DNA are obtained in thermal denaturation
experiments, which depend on several assumptions. Here we report measurements
of the DNA base-pair free energies based on a simplified system, the mechanical
unzipping of single DNA molecules. By combining experimental data with a
physical model and an optimization algorithm for analysis, we measure the 10
unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision
over two orders of magnitude of monovalent salt concentration. We find an
improved set of standard energy values compared with Unified Oligonucleotide
energies and a unique set of 10 base-pair-specific salt-correction values. The
latter are found to be strongest for AA/TT and weakest for CC/GG. Our new
energy values and salt corrections improve predictions of DNA unzipping forces
and are fully compatible with melting temperatures for oligos. The method
should make it possible to obtain free energies, enthalpies and entropies in
conditions not accessible by bulk methodologies.Comment: Main text: 27 pages, 4 figures, 2 tables. Supporting Information: 51
pages, 19 figures, 4 table
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