The possible role of solitonic processes during A to B conformational changes in DNA

Khan, Angshutosh; Bhaumik, Debajyoti; Dutta-Roy, Binayak

doi:10.1007/bf02469305

Cited by 20 publications

(8 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Yomosa [3] proposed a plane base rotator model (a generalized Frenkel-Kontorova [4] model) by taking into account the rotational motion of bases in a plane normal to the helical axis, and Takeno and Homma generalized the above model [5]. Later, using this model, several authors found solitons as governing the fluctuation of DNA double helix between an open state and its equilibrium states [6][7][8][9]. The oscillations of the strands, in all the above models, have been shown to be governed by the completely integrable sine-Gordon (sG) equation.…”

Section: Introductionmentioning

confidence: 99%

Energy localization in an anharmonic twist-opening model of DNA dynamics

Tabi

2010

J. Phys.: Condens. Matter

View full text Add to dashboard Cite

Energy localization is investigated in the framework of the anharmonic twist-opening model proposed by Cocco and Monasson. This model includes the coupling between opening and twist that result from the helicoidal geometry of B-DNA. I first reduce the corresponding two-component model to its amplitude equations, which have the form of coupled discrete nonlinear Schrödinger (DNLS) equations, and I perform the linear stability analysis of the plane waves, solutions of the coupled DNLS equations. It is shown that the stability criterion deeply depends on the stiffness of the molecule. Numerical simulations are carried out in order to verify analytical predictions. It results that increasing the value of the molecule stiffness makes the energy patterns long-lived and highly localized. This can be used to explain the way enzymes concentrate energy on specific sequences of DNA for the base-pairs to be broken. The role of those enzymes could therefore be to increase the stiffness of closed regions of DNA at the boundaries of an open state.

show abstract

Section: Introductionmentioning

confidence: 99%

Energy localization in an anharmonic twist-opening model of DNA dynamics

Tabi

2010

J. Phys.: Condens. Matter

View full text Add to dashboard Cite

show abstract

“…Yomosa [4,5] proposed a plane base rotator model by taking into account the rotational motion of bases in a plane normal to the helical axis, and Takeno and Homma generalized the same [6,7,8]. Later using this model, several authors found solitons to govern the fluctuation of DNA double helix between an open state and its equilibrium states [9,10,11,12,13,14].…”

Section: Introductionmentioning

confidence: 99%

Nonlinear molecular excitations in a completely inhomogeneous DNA chain

Daniel

Vasumathi

2008

Physics Letters A

View full text Add to dashboard Cite

show abstract

“…[11]) using Toda lattice model in which two types of internal motions namely, transverse motion along the hydrogen bond direction and longitudinal motion along the backbone direction were found to contribute to DNA denaturation process in terms of travelling solitary waves and standing waves. These localized nonlinear excitations further explain conformation transition [12,13,14], long range interaction of kink solitons in the double chain [15,16], regulation of transcription [15,17], denaturation [10] and charge transport in terms of polarons and bubbles [18]. Some of them have been successfully used for interpreting experimental data related to microwave absorption [19,20].…”

Section: Introductionmentioning

confidence: 99%

Perturbed soliton excitations in the DNA double helix

Daniel

Vasumathi

2007

Physica D: Nonlinear Phenomena

View full text Add to dashboard Cite

We study nonlinear dynamics of inhomogeneous DNA double helical chain under dynamic plane-base rotator model by considering angular rotation of bases in a plane normal to the helical axis. The DNA dynamics in this case is found to be governed by a perturbed sine-Gordon equation while taking into account the interstrand hydrogen bonding energy between bases and the intrastrand inhomogeneous stacking energy and by making an analogy with the Heisenberg model of the Hamiltonian of an inhomogeneous anisotropic spin ladder with ferromagnetic legs and antiferromagnetic rung coupling. In the homogeneous limit the dynamics is governed by the kink-antikink soliton of the sine-Gordon equation which represents the formation of open state configuration in DNA double helix. The effect of inhomogeneity in stacking energy in the form of localized and periodic variations on the formation of open states in DNA is studied under perturbation. The perturbed soliton is obtained using a multiple scale soliton perturbation theory by solving the associated linear eigen value problem and by constructing the complete set of eigen functions. The inhomogeneity in stacking energy is found to modulate the width and speed of the soliton depending on the nature of inhomogeneity. Also it introduces fluctuations in the form of train of pulses or periodic oscillations in the open state configuration.

show abstract

The possible role of solitonic processes during A to B conformational changes in DNA

Cited by 20 publications

References 12 publications

Energy localization in an anharmonic twist-opening model of DNA dynamics

Energy localization in an anharmonic twist-opening model of DNA dynamics

Nonlinear molecular excitations in a completely inhomogeneous DNA chain

Perturbed soliton excitations in the DNA double helix

Contact Info

Product

Resources

About