Microscopical approach to the helix–coil transition in DNA

Morozov, V. F.; Мамасахлисов, Е. Ш.; Hayryan, Shura; Hu, Chin–Kun

doi:10.1016/s0378-4371(00)00054-6

Cited by 31 publications

(31 citation statements)

References 15 publications

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“…However, contrary to those studies we did not observe an increase in stability with increasing α on the right side of the phase diagram. This might be due to specific features of DNA associated with large loops which were omited in our studies [11]. Another possible source of this discrepancy could be the polyelectrolyte nature of polynucleotides.…”

Section: B Reentrance In Polynucleotidesmentioning

confidence: 69%

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Competition for hydrogen-bond formation in the helix-coil transition and protein folding

et al. 2011

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The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds.The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA.

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Section: B Reentrance In Polynucleotidesmentioning

confidence: 69%

“…A number of different approaches to describing the helix-coil transition in biopolymers have appeared in the literature; many of them based on spin models [3][4][5][6][7][8][9][10][11][12]. As shown in Refs.…”

Section: Introductionmentioning

confidence: 99%

Competition for hydrogen-bond formation in the helix-coil transition and protein folding

et al. 2011

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“…To be more precise, the quantity U is the energy of the helical state of one base pair, i.e., it includes also the stacking of bases (Morozov et al, 2000). Here an approximation is done that the stacking interactions are the same for all base pairs throughout the chain.…”

Section: The Model Of the Linear Dnamentioning

confidence: 99%

“…It appeared that the secular equation of the DNA Hamiltonian may be written in exactly the same form as for polypeptide chain in which the characteristic length of hydrogen bond is replaced by some characteristic length of DNA molecule. The model was published in (Morozov et al, 2000) and will be reviewed briefly in Sec. II of the present paper.…”

Section: Introductionmentioning

confidence: 99%

Helix–coil transition in closed circular DNA

Morozov¹,

Мамасахлисов²,

Grigoryan³

et al. 2005

Physica A: Statistical Mechanics and its Applications

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A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The basic assumption is that the reduced energy of the hydrogen bond is not constant through the transition process but depends effectively on the fraction of already broken bonds. A transformation formula is obtained which relates the temperature of ccDNA at a given degree of helicity during the transition to the temperature of the corresponding linear chain at the same degree of helicity.The formula provides a simple method to calculate the melting curve for the ccDNA from the experimental melting curve of the linear DNA with the same nucleotide sequence.

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“…Then it was shown that the same approach could be applied to DNA if ignore large-scale loop factor [26].…”

Section: Basic Model (Gmpc)mentioning

confidence: 99%

Stacking and hydrogen bonding: DNA cooperativity at melting

et al. 2004

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By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition in both polypeptides and polynucleotides. In the framework of the GMPC we show that correctly introduced nearestneighbor stacking interactions against the background of hydrogen bonding lead to increased stability (melting temperature) and, unexpectedly, to decreased cooperativity (maximal correlation length). The increase in stability is explained as due to an additional stabilizing interaction (stacking) and the surprising decrease in cooperativity is seen as a result of mixing ofcontributions of hydrogen bonding and stacking.

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Microscopical approach to the helix–coil transition in DNA

Cited by 31 publications

References 15 publications

Competition for hydrogen-bond formation in the helix-coil transition and protein folding

Competition for hydrogen-bond formation in the helix-coil transition and protein folding

Helix–coil transition in closed circular DNA

Stacking and hydrogen bonding: DNA cooperativity at melting

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