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题名: Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions
作者: Ou-Yang, ZC ;  Zhou, HJ ;  Ou-Yang, ZC
刊名: BIOPHYSICAL JOURNAL
出版日期: 2001
卷号: 81, 期号:2, 页码:1133-1143
关键词: 16S ;  SUPERCOILED DNA ;  MOLECULES ;  ELASTICITY ;  POLYMERASE ;  MECHANICS ;  DYNAMICS ;  SYSTEMS ;  FORCE ;  16S
学科分类: Physics
通讯作者: Zhang, Y , Donald Danforth Plant Sci Ctr, Lab Comp Genom, 893 N Warson Rd, St Louis, MO 63141 USA.
部门归属: Donald Danforth Plant Sci Ctr, Lab Comp Genom, St Louis, MO 63141 USA; Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China; Max Planck Inst Colloids & Interfaces, Div Theory, D-14424 Potsdam, Germany
英文摘要: Recent single-macromolecule observations revealed that the force/extension characteristics of single-stranded DNA (ssDNA) are closely related to solution ionic concentration and DNA sequence composition. To understand this, we studied the elastic property of ssDNA through the Monte Carlo implementation of a modified freely jointed chain (FJC), with electrostatic, base-pairing, and base-pair stacking interactions all incorporated. The simulated force-extension profiles for both random and designed sequences have attained quantitative agreements with the experimental data. In low-salt solution, electrostatic interaction dominates, and at low forces, the molecule can be more easily aligned than an unmodified FJC. In high-salt solution, secondary hairpin structure appears in ssDNA by the formation of base pairs between complementary bases, and external stretching causes a hairpin-coil structural transition, which is continuous for ssDNA made of random sequences. In designed sequences such as poly(dA-dT) and poly(dG-dC), the stacking potential between base pairs encourages the aggregation of base pairs into bulk hairpins and makes the hairpin-coil transition a discontinuous (first-order) process. The sensitivity of elongation to the base-pairing rule is also investigated. The comparison of modeling calculations and the experimental data suggests that the base pairing of single-stranded polynucleotide molecules tends to form a nested and independent planar hairpin structure rather than a random intersecting pattern.
收录类别: SCI
原文出处: 查看原文
WOS记录号: WOS:000170152000045
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/13690
Appears in Collections:理论物理所1978-2010年知识产出_期刊论文

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Recommended Citation:
Ou-Yang, ZC,Zhou, HJ,Ou-Yang, ZC. Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions[J]. BIOPHYSICAL JOURNAL,2001,81(2):1133-1143.
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