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Liu, F; Dai, LR; Ou-Yang, ZC; Liu, F , Chinese Acad Sci, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
Theory for the force-stretched double-stranded chain molecule
Source PublicationJOURNAL OF CHEMICAL PHYSICS
KeywordSecondary Structure Polymer-molecules Hairpin Formation Dna-molecules Rna Sequence Configuration Denaturation Energy Shape
AbstractWe modify and extend the recently developed statistical mechanical theory of chain molecules having noncovalent double-stranded conformations, as in RNA or single-stranded DNA, and beta sheets in protein, to the force-stretched case as in a typical single-molecule experiment. The conformations of double-stranded regions of the molecules are calculated based on polymer graph-theoretic approach [S.-J. Chen and K. A. Dill, J. Chem. Phys. 109, 4602 (1998)], while the unpaired single-stranded regions are treated as self-avoiding walks. Two classes of conformations-the hairpin conformations and RNA secondary structures-are explored. For the hairpin conformations, all possible end-to-end distances corresponding to the different types of double-stranded regions are enumerated exactly. For the RNA secondary structures, a recursive formula incorporating the secondary structure and end-to-end distribution has been derived. The sequence dependence and excluded volume interaction are taken into account explicitly. Using the extended theory, we investigate the extension-force and force-extension curves, distribution of the extensions at fixed forces, and reentering phenomenon, respectively. We find that the mechanical behaviors of homogeneous chains of hairpin conformations and secondary structures are quite different: the unfolding of the hairpin case is two state, while the unfolding of the latter is one state. In addition, a reentering transition is observed in hairpin conformations. (C) 2003 American Institute of Physics.
2003
ISSN0021-9606
Volume119Issue:15Pages:8112-8123
Subject AreaPhysics
Indexed BySCI
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Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/13203
Collection理论物理所科研产出_SCI论文
Corresponding AuthorLiu, F , Chinese Acad Sci, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
Recommended Citation
GB/T 7714
Liu, F,Dai, LR,Ou-Yang, ZC,et al. Theory for the force-stretched double-stranded chain molecule[J]. JOURNAL OF CHEMICAL PHYSICS,2003,119(15):8112-8123.
APA Liu, F,Dai, LR,Ou-Yang, ZC,&Liu, F , Chinese Acad Sci, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China..(2003).Theory for the force-stretched double-stranded chain molecule.JOURNAL OF CHEMICAL PHYSICS,119(15),8112-8123.
MLA Liu, F,et al."Theory for the force-stretched double-stranded chain molecule".JOURNAL OF CHEMICAL PHYSICS 119.15(2003):8112-8123.
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