title: Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions.
abstract: 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.
authors.affiliation: Institute of Theoretical Physics, The Chinese Academy of Sciences, Beijing 100080, China. yzhang@danforthcenter.org
authors.forename: Y
authors.initials: Y
authors.lastname: Zhang
authors.forename: H
authors.initials: H
authors.lastname: Zhou
authors.forename: Z C
authors.initials: ZC
authors.lastname: Ou-Yang
mesh_terms: D020029:Base Pairing; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism*; D004548:Elasticity; D008958:Models, Molecular; D009010:Monte Carlo Method; D016012:Poisson Distribution; D055672:Static Electricity
chemical_list: D004277:DNA, Single-Stranded