A model for separation and melting of deoxyribonucleic acid in replication and transcription processes

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	A model for separation and melting of deoxyribonucleic acid in replication and transcription processes
	P. Xiao-Feng; F. Ynan-Ping
	2008
发表期刊	Journal of Biomolecular Structure & Dynamics
ISSN	0739-1102
卷号	25 期号:4 页码:435-451
摘要	In order to explain the denaturation and melting in replication and transcription of deoxyribonucleic acid (DNA) at physiological temperature, we propose a dynamical model on the basis of structure and motion of DNA under the actions of energy released in hydrolysis of adenosine triphosphate (ATP) and enzymes. The model admits three degrees of freedom per base pair: two displacement variables associated with the vibrations of hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable describing the rotation of base. The important role of hydrogen atom in the hydrogen bonds is stressed in this model. The Hamiltonian of the intact double helix system is given first, subsequently the equations of motion and solutions of a melting system are developed. The solutions represent the excited states formed by the displacements of hydrogen atoms and bases and the rotations of bases, arising from the energy absorbed by DNA, respectively. The results obtained show that the displacements of hydrogen atoms increase with time and along the helix. Once the displacements of hydrogen atoms and rotations of bases reach to certain limits, the hydrogen bonds are disrupted, and the two double helical strands of DNA are separated, a melting state in the replication or transcription process occurs. The properties of thermal motion of hydrogen atoms in this state at physiological temperature is further studied by using a transfer integral method and the thermodynamic properties such as free energy and entropy of the thermally excited state are obtained in the process. Values of characteristic parameters and critical temperature of melting in transcription process are derived. Finally the validity of the theory was demonstrated through comparison between experimental and theoretical data of specific heat and force of phase transition. This investigation is helpful to understand mechanism and essence of the replication or transcription process and promote quantitative description of these processes.
部门归属	[xiao-feng, pang] univ elect sci & technol china, inst life sci & technol, chengdu 610065, peoples r china. [xiao-feng, pang] chinese acad sci, int ctr mat phys, shenyang 110015, peoples r china. [ynan-ping, feng] natl univ singapore, dept phys, singapore 117542, singapore.;xiao-feng, p (reprint author), univ elect sci & technol china, inst life sci & technol, chengdu 610065, peoples r china;pangxf2006@yaboo.com.cn
关键词	Dna Double Helix Bonded Molecular-systems Consistent Phonon Theory One-dimensional Model Peyrard-bishop Model Statistical-mechanics Hydrogen-exchange Nonlinear Model Proton-transfer Temperature-dependence
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WOS记录号	WOS:000252488300012
引用统计
文献类型	期刊论文
条目标识符	http://ir.imr.ac.cn/handle/321006/33228
专题	中国科学院金属研究所
推荐引用方式 GB/T 7714	P. Xiao-Feng,F. Ynan-Ping. A model for separation and melting of deoxyribonucleic acid in replication and transcription processes[J]. Journal of Biomolecular Structure & Dynamics,2008,25(4):435-451.
APA	P. Xiao-Feng,&F. Ynan-Ping.(2008).A model for separation and melting of deoxyribonucleic acid in replication and transcription processes.Journal of Biomolecular Structure & Dynamics,25(4),435-451.
MLA	P. Xiao-Feng,et al."A model for separation and melting of deoxyribonucleic acid in replication and transcription processes".Journal of Biomolecular Structure & Dynamics 25.4(2008):435-451.