The probability analysis of opening of DNA

Srivastava, Shikha; Singh, Navin

doi:10.1063/1.3563633

Cited by 36 publications

(15 citation statements)

References 40 publications

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“…The latter also display the well known multistep melting features in the specific heat plots mirroring the fact that segments of the molecule open at different temperatures with AT-rich regions driving the bubble formation at relatively lower temperatures. Interestingly a recent study [34], based on the extended transfer matrix method [35], which focusses on the same heterogeneous sequences considered in Ref. [33], finds similar results regarding the temperature location of the main specific heat peaks.…”

Section: Introductionsupporting

confidence: 57%

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: Introductionsupporting

confidence: 57%

Thermodynamics of twisted DNA with solvent interaction

Zoli

2011

The Journal of Chemical Physics

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“…These include the effects of randomness in interaction, or force [28][29][30][31], semiflexibility [32], and finite length [33,34]. Many details of the transition have also been studied, like various distributions [35], temperature dependence [36], different types of noise [37,38], role of ensembles [39]. The dependence of melting on the nature of the space has also been studied via the choice of different fractal lattices [40][41][42][43][44], showing the possible variations in the melting transition.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic relations for DNA phase transitions

Sadhukhan

Bhattacharjee

2014

Indian J Phys

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The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The thermodynamic approach is based on the hypothesis of impenetrability of the force in the zipped state. The melting and the unzipping transitions are considered in the same framework and compared with the existing statistical model results. The analysis is then extended to a possible continuous unzipping transition.

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“…Precisely for the same sequences considered in Ref. [38], a recent analysis [39] based on the extended transfer matrix approach [40] finds consistent results regarding the temperature location of the main peaks in the specific heat profiles.…”

Section: Introductionmentioning

confidence: 88%

Stacking interactions in denaturation of DNA fragments

Zoli

2011

Eur. Phys. J. E

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A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the adenine-thymine rich portions of the fragment. The harmonic stacking coupling shifts, along the T -axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.

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The probability analysis of opening of DNA

Cited by 36 publications

References 40 publications

Thermodynamics of twisted DNA with solvent interaction

Thermodynamics of twisted DNA with solvent interaction

Thermodynamic relations for DNA phase transitions

Stacking interactions in denaturation of DNA fragments

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