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Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions
Ou-Yang, ZC; Zhou, HJ; Zhang, Y , Donald Danforth Plant Sci Ctr, Lab Comp Genom, 893 N Warson Rd, St Louis, MO 63141 USA.
2001
发表期刊BIOPHYSICAL JOURNAL
ISSN0006-3495
卷号81期号:2页码:1133-1143
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.
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
关键词16s Supercoiled Dna Molecules Elasticity Polymerase Mechanics Dynamics Systems Force 16s
学科领域Physics
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收录类别SCI
WOS记录号WOS:000170152000045
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被引频次:101[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/13690
专题理论物理所1978-2010年知识产出
通讯作者Zhang, Y , Donald Danforth Plant Sci Ctr, Lab Comp Genom, 893 N Warson Rd, St Louis, MO 63141 USA.
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Ou-Yang, ZC,Zhou, HJ,Zhang, Y , Donald Danforth Plant Sci Ctr, Lab Comp Genom, 893 N Warson Rd, St Louis, MO 63141 USA.. Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions[J]. BIOPHYSICAL JOURNAL,2001,81(2):1133-1143.
APA Ou-Yang, ZC,Zhou, HJ,&Zhang, Y , Donald Danforth Plant Sci Ctr, Lab Comp Genom, 893 N Warson Rd, St Louis, MO 63141 USA..(2001).Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions.BIOPHYSICAL JOURNAL,81(2),1133-1143.
MLA Ou-Yang, ZC,et al."Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and base-pair stacking interactions".BIOPHYSICAL JOURNAL 81.2(2001):1133-1143.
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