Stretching Single-Stranded DNA: Interplay of Electrostatic, Base-Pairing, and Base-Pair Stacking Interactions

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 implementat...

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Bibliographic Details
Published in:Biophysical journal 2001-08, Vol.81 (2), p.1133-1143
Main Authors: Zhang, Yang, Zhou, Haijun, Ou-Yang, Zhong-Can
Format: Article
Language:English
Subjects:
Base Pairing
Biology
Deoxyribonucleic acid
DNA
DNA, Single-Stranded - chemistry
DNA, Single-Stranded - metabolism
Elasticity
Ions
Models, Molecular
Molecules
Monte Carlo Method
Monte Carlo simulation
Physics
Poisson Distribution
Static Electricity
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Summary: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.
ISSN:0006-3495
1542-0086
DOI:10.1016/S0006-3495(01)75770-0