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Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?
Zhou, HJ; Zhang, Y; Zhou, HJ , Max Planck Inst Colloids & Interfaces, D-14424 Potsdam, Germany.
2001
发表期刊JOURNAL OF CHEMICAL PHYSICS
ISSN0021-9606
卷号114期号:19页码:8694-8700
摘要Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base pairing and base-pair stacking interactions, and a threshold external force is needed to pull the hairpinned structure into a random coiled one. The base-pair stacking interaction in the ssDNA chain makes this hairpin-coil conversion a discontinuous (first-order) phase transition process characterized by a force plateau in the force-extension curve, while lowering this potential below some critical level turns this transition into continuous (second-order) type, no matter how strong the base-pairing interaction is. The phase diagram (including hairpin-I, -II, and random coil) is discussed as a function of stacking potential and external force. These results are in quantitative agreement with recent experimental observations of different ssDNA sequences, and they reveal the necessity to consider the base-pair stacking interactions in order to understand the structural formation of RNA, a polymer designed by nature itself. The theoretical method used may be extended to study the long-range interaction along double-stranded DNA caused by the topological constraint of fixed linking number. (C) 2001 American Institute of Physics.
部门归属Max Planck Inst Colloids & Interfaces, D-14424 Potsdam, Germany; Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
关键词Double-stranded Dna Rna Secondary Structure Supercoiled Dna Single-molecule Entropic Elasticity Mechanics Model Polymerase
学科领域Physics
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收录类别SCI
WOS记录号WOS:000168440400053
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文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/12751
专题理论物理所1978-2010年知识产出
通讯作者Zhou, HJ , Max Planck Inst Colloids & Interfaces, D-14424 Potsdam, Germany.
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Zhou, HJ,Zhang, Y,Zhou, HJ , Max Planck Inst Colloids & Interfaces, D-14424 Potsdam, Germany.. Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?[J]. JOURNAL OF CHEMICAL PHYSICS,2001,114(19):8694-8700.
APA Zhou, HJ,Zhang, Y,&Zhou, HJ , Max Planck Inst Colloids & Interfaces, D-14424 Potsdam, Germany..(2001).Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?.JOURNAL OF CHEMICAL PHYSICS,114(19),8694-8700.
MLA Zhou, HJ,et al."Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?".JOURNAL OF CHEMICAL PHYSICS 114.19(2001):8694-8700.
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