Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process

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	Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process
	X. F. Pang; Y. P. Feng; H. W. Zhang; S. M. Assad
	2006
发表期刊	Journal of Physics-Condensed Matter
ISSN	0953-8984
卷号	18 期号:39 页码:9007-9030
摘要	Biological functions and genetic features of DNA, such as duplication, transcription and gene expression, are mainly determined by its structure, but depend also on the temperature and features of solution, such as salt concentration. We study the influence of temperature and salt concentration on the conformation changes and transcription of DNA by using a new dynamical model. This new model admits three degrees of freedom per base- pair: two displacement variables related to the vibrations of hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable related to the rotation of base. The important role of motion of hydrogen atom in the hydrogen bonds is specially stressed in this model. This is helpful to reveal the mechanism of transcription of DNA. According to their properties of motion, we first give the Hamiltonian of the system, corresponding equations of motion and their soliton-solutions. The solitons are the excitation states formed by the displacements of hydrogen atoms and bases and the rotations of bases, arising from the energy absorbed by DNA, in the systems, respectively. By applying the transfer integral method we obtain the thermodynamic properties (e.g. free energy and entropy) of the thermal excitation state of DNA at the biological temperature in this model. According to the properties of these thermodynamic functions obtained we study the mechanism and processes of melting and transcription of DNA with the aid of the transforms of energy carried by the soliton in such a case. We further give the properties of the transcription of DNA with the help of the average value of the mean square of displacement of hydrogen atom, and the values of subcritical temperature and force of the phase transition are also found. Finally, we conclude that the transcription of DNA not only depends directly on the properties of its structure and of energy absorbed by it, but also is influenced by the temperature and salt concentration in the solution of DNA, which is consistent with experimental data. Therefore this new model not only can predict the transcription of DNA, but also can give the relationship among the conformation changes and the temperature and salt concentration. Finally we discuss in simple terms the influences of water or solution around DNA on its dynamics and further point out the defects and limitations of the new model of the dynamics of DNA and its direction of development.
部门归属	univ elect sci & technol china, inst life sci & technol, chengdu 610065, peoples r china. chinese acad sci, int ctr mat phys, shenyang 110015, peoples r china. natl univ singapore, dept phys, singapore 119260, singapore. univ elect sci & technol china, sch microelectron & solid state elect, chengdu 610054, peoples r china.;pang, xf (reprint author), univ elect sci & technol china, inst life sci & technol, chengdu 610065, peoples r china
关键词	Dna Double Helices Thermally Generated Solitons Breather Trapping Mechanism Consistent Phonon Theory Klein-gordon Lattices One-dimensional Model Peyrard-bishop Model Statistical-mechanics Hydrogen-bond Vibrational-modes
URL	查看原文
WOS记录号	WOS:000241269800032
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.imr.ac.cn/handle/321006/34420
专题	中国科学院金属研究所
推荐引用方式 GB/T 7714	X. F. Pang,Y. P. Feng,H. W. Zhang,et al. Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process[J]. Journal of Physics-Condensed Matter,2006,18(39):9007-9030.
APA	X. F. Pang,Y. P. Feng,H. W. Zhang,&S. M. Assad.(2006).Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process.Journal of Physics-Condensed Matter,18(39),9007-9030.
MLA	X. F. Pang,et al."Dynamical features of deoxyribonucleic acid and configuration transition in the transcription process".Journal of Physics-Condensed Matter 18.39(2006):9007-9030.