Nonlinear Analysis of the Dynamics of DNA Breathing

Peyrard, Michel; Cuesta‐López, Santiago; James, Guillaume

doi:10.1007/s10867-009-9127-2

Cited by 72 publications

(89 citation statements)

References 22 publications

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“…As the energy per hydrogen bond is about 15meV , I set for AT − and GC− bases respectively D AT = 30meV and D GC = 45meV . ATbase pairs have larger displacements than GC-base pairs, then the inverse lengths are taken as a AT = 4.2Å −1 and a GC = 5Å −1 while slightly different values can be found in the literature [47,48]. Note that the plateau in V M (y n ) has a relevant physical implication: once all base pair displacements are larger than a −1…”

Section: Hamiltonian Modelmentioning

confidence: 99%

Thermodynamics of twisted DNA with solvent interaction

Zoli

2011

The Journal of Chemical Physics

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The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over ∼ 10 7 − 10 8 base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.

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Section: Hamiltonian Modelmentioning

confidence: 99%

Thermodynamics of twisted DNA with solvent interaction

Zoli

2011

The Journal of Chemical Physics

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“…For the equilibrium calculations, we used PBD model and found the denaturation point in thermal as well as in constant force ensembles. For the homogeneous chain, we found that there is a segment (4)(5)(6)(7)(8)(9)(10)(11)(12) of the chain where T m is unaffected by the location of the defect in the chain. In case of heterogeneous chain, there is no plateau but it matters on a location whether there is an AT pair or a GC pair.…”

Section: Discussionmentioning

confidence: 89%

“…Although the model ignores the helicoidal structure of the dsDNA molecule, it has enough details to analyze mechanical behavior at the few angstrom scale relevant to molecular-biological events [10]. The Hamiltonian for the considered system of N base pairs unit is written as,…”

Section: The Modelmentioning

confidence: 99%

“…The hydrogen bonding strength for these two base pairs is not same as the AT base pair has two hydrogen bonds while GC base pair has three hydrogen bonds. The approximate ratio of GC and AT bond strengths varies from 1.2 to 1.5 as mentioned by various research groups [3][4][5][6][7][8][9][10][11][12]. In the absence of the complementary base on the opposite strand, the pairing between the two bases is absent.…”

Section: Introductionmentioning

confidence: 99%

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Pulling short DNA molecules having defects on different locations

Singh

2015

Phys. Rev. E

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We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.

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“…The PB model and some variations [5][6][7] have been used to study the dynamics [8][9][10] and the thermodynamics [11][12][13] of DNA. From the dynamical point of view, there are studies about localized energy modes [14] that were identified as precursors of the denaturation and transcription process.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Lattice Size, Energy Density and Denaturation for a One-Dimensional DNA Model

Slade¹,

Ribeiro²,

Filho³

et al. 2012

WJM

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There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is studied under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The thermodynamics analysis using the transfer integral operator method is briefly reviewed. In particular, the lattice size is discussed and a conjecture about the minimum energy to denaturation is proposed. In terms of the dynamical aspects of the model, the equations of motion for the system are integrated and the results determine the energy density where the denaturation occurs. The behavior of the lattice near the phase transition is analyzed. The relation between the thermodynamical and dynamical results is discussed.

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Nonlinear Analysis of the Dynamics of DNA Breathing

Cited by 72 publications

References 22 publications

Thermodynamics of twisted DNA with solvent interaction

Thermodynamics of twisted DNA with solvent interaction

Pulling short DNA molecules having defects on different locations

Analysis of Lattice Size, Energy Density and Denaturation for a One-Dimensional DNA Model

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