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1.
A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation transition upon heating. However, in circular DNA chains and some experimental setups that manipulate single DNA molecules, the total number of turns (linking number) is constant at all times. The consequences of this additional topological invariant on the melting behaviour are nontrivial. Below, we investigate the melting characteristics of a homogeneous DNA where the linking number along the melting curve is preserved by supercoil formation in duplex portions. We obtain the mass fraction and the number of loops and supercoils below and above the melting temperature. We also argue that a macroscopic loop appears at T c and calculate its size as a function of temperature. 相似文献
2.
A. V. Grigoryan A. V. Badasyan E. Sh. Mamasakhlisov V. F. Morozov 《Physics of Atomic Nuclei》2005,68(10):1685-1688
The order-disorder (helix-coil) transition in circular closed DNA (ccDNA) is described on the basis of the open chain DNA (ocDNA) model, proposed earlier, which considers the transition as loop formation. The Hamiltonian of the ccDNA model is constructed on the basis of the open chain model taking into account topological restrictions. These restrictions are taken into account through hydrogen bond reduced energy dependence on the fraction of broken hydrogen bonds in the macromolecule. The invariance of the order parameter (helicity degree) has been shown for ocDNA and ccDNA. This invariance results in the interdependence between temperatures of ocDNA and ccDNA with the same value of helicity degree. The dependence can be obtained with the help of the derivative of reduced energy of hydrogen bonding dependence on instantaneous denaturation degree. Thus, it has been shown that the melting curve of ccDNA can be obtained from the consequent curve of ocDNA through the redefinition of temperature scale. The calculated and experimentally measured melting curves have been compared under inversion conditions and qualitative agreement between them is found. 相似文献
3.
We investigate the statistical mechanics properties
of a nonlinear dynamics model of the denaturation of the DNA
double-helix and study the effects of salt concentration and
temperature on denaturation transition of DNA. The specific heat,
entropy, and denaturation temperature of the system versus salt concentration
are obtained. These results show that the denaturation of DNA
not only depends on the temperature but also is influenced by
the salt concentration in the solution of DNA, which are in agreement
with experimental measurement. 相似文献
4.
Y. Kafri D. Mukamel L. Peliti 《The European Physical Journal B - Condensed Matter and Complex Systems》2002,27(1):135-146
Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the
melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an
approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound
segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different
loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account
in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by
exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity
of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition,
which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under
equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are
thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size
distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition
is approached. We evaluate these critical properties within our approach.
Received 21 August 2001 and Received in final form 26 January 2002 相似文献
5.
We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent c, for which we find the new value c = 4 nu-1/2 such that the transition is second order with c = 1.85 < 2 in d = 3. We show that a finite stretching force F destabilizes DNA, corresponding to a lower melting temperature T(F), in agreement with single-molecule DNA stretching experiments. 相似文献
6.
Using magnetic tweezers, we study in real time the condensation of single DNA molecules under tension. We find that DNA condensation occurs via discrete nucleated events. By measuring the influence of an imposed twist, we show that condensation is initiated by the formation of a plectonemic supercoil. This demonstrates a strong interplay between the condensation transition and externally imposed mechanical constraints. 相似文献
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9.
M. Baiesi E. Orlandini A.L. Stella 《The European Physical Journal B - Condensed Matter and Complex Systems》2002,28(4):467-473
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded
DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the linking number
to fluctuate freely in equilibrium we see that the linking probability undergoes an abrupt variation (first-order) at the
denaturation transition, and stays close to 1 in the whole native phase. The average linking number is almost zero in the
denatured phase and grows as the square root of the chain length, N, in the native phase. The writhe of the two strands grows as in both phases.
Received 8 May 2002 Published online 13 August 2002 相似文献
10.
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles, and the possibility of a two-state transition are studied. 相似文献
11.
Y. Sh. Mamasakhlisov A. P. Antonyan A. Y. Mamasakhlisov Sh. A. Tonoyan P. H. Vardevanyan 《Journal of Contemporary Physics (Armenian Academy of Sciences)》2017,52(2):173-179
The melting of the DNA–ligand complex is considered theoretically for the ligands binding with the DNA by two mechanisms. The obtained results describe the experimentally observed behavior of such quantities as the denaturation degree and the correlation length depending on the concentration of ligands. It is shown that the heat and cold denaturations of the DNA–ligand complexes exhibit the same cooperativity, as the heat denaturation of the pure DNA. At the same time, the temperature range of the cold denaturation is essentially narrower than the interval for the heat denaturation of the pure DNA and the DNA–ligand complexes. 相似文献
12.
Experimental and theoretical results on the helix-coil transition of DNA are reviewed. The theoretical model of the transition is described, and the influence of heterogeneous base pair stacking, and strand dissociation on the predicted melting transition is examined. New experimental transition data on seven DNAs, 154–587 base pairs (bp) long, are reported and compared with theoretical calculations. We review and evaluate previous studies on long DNAs (≥1000 bp) as well as previous and recent results on short DNAs. The comparison of theory with equilibrium melting curves of short DNAs indicates that base pair sequence has a relatively small influence on the stacking free energy. Excellent agreement is obtained between theory and equilibrium transitions of 14 out of 15 fragments 80–587 pb. The deviation between theory and experiment for a 516 bp DNA can be attributed to the formation of stem-loop structures. This may provide the explanation for inconsistent results observed with long DNAs. The effect of single base pair changes on DNA transitions is discussed. Current views on fluctuational opening of base pairs at temperatures below the transition are described. 相似文献
13.
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B-DNA, supercoiling, optimally stable torque, and the overstretching transition as force-induced DNA melting. Agreement with available single molecule manipulation experiments is excellent. 相似文献
14.
Summary We have considered a model of a lattice gas defined on a periodic tangled chain to study the DNA denaturation by a modified
transfer matrix method. By using an iterative algorithm we have obtained numerically different kinds of melting curves for
different configurations of the tangled chain and different types of interactions. In some special cases of configurations
and interactions we have found the same melting curves, which we have obtained before studying some simple lattice gas models,
using different techniques. This more generalized model and the new results could be useful for the experimental investigations. 相似文献
15.
Clément Dombry 《Journal of statistical physics》2005,120(3-4):695-719
We consider Benham’s model for strand separation in supercoiled circular DNA. This is a mean field model in external inhomogeneous
field, conditioned to small values of the perimeter. Under some conditions on the external field, we prove a large deviations
principle for the distribution of the magnetization under the Gibbs measure. The rate function strongly depends on the structure
of the external field. It allows us to prove a law of large numbers and to study denaturation as a function of the temperature
and the superhelical density. 相似文献
16.
Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on the denaturation
profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state.
The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian.
The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also
examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at
different parts of the chain. 相似文献
17.
Errami J Peyrard M Theodorakopoulos N 《The European physical journal. E, Soft matter》2007,23(4):397-411
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation
and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative
calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is
modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of
a diffusion-controlled motion in an effective free-energy landscape. Melting profiles, dependence of melting temperature on
loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA
beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy
of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single
strands of DNA or RNA are discussed. 相似文献
18.
The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome. 相似文献
19.
Zoli M 《J Phys Condens Matter》2012,24(19):195103
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation. 相似文献
20.
《光谱学快报》2013,46(6):781-797
ABSTRACT In this paper, the noncovalent binding of the cationic reagent lucigenin (LC) to DNA was investigated using spectroscopic methods. The results from absorption, circular dichroism and fluorescence studies demonstrated that LC could intercalate into the helix of DNA. Polarization and melting studies further supported the intercalation binding of LC with DNA. The binding constant was obtained by varying the DNA concentration, while keeping the concentration of LC constant. It was of the order of 104 mol?1 L in DNA base pairs. The experiment also showed that electrostatic interaction played a significant role in the intercalation of LC with DNA. It is supposed to be because of being attracted first by anionic DNA that LC can be intercalated into the interior of the DNA double helix. This research offers a new intercalation functional group to DNA-targeted drug design. 相似文献