title: Unfolding and unzipping of single-stranded DNA by stretching.
abstract: We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of base pairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of chain elasticity. In a generic case, we show that the stretching curve of single-stranded DNA exhibits two distinct features: the second-order "unfolding" phase transition, and a sharp crossover, reminiscent of the first-order "unzipping" transition in double-stranded DNA. We apply the theory to the particular cases of wormlike chain and freely jointed chain models, and discuss the universal and model-dependent features of the mechanical response of single-stranded DNA. In particular, we show that variation of the width of the unzipping crossover with interaction strength is very sensitive to the energetics of hairpin loops. This opens another way of testing the elastic properties of ssDNA.
authors.affiliation: Michigan Center for Theoretical Physics and Department of Physics, University of Michigan, 500 East University Avenue, Ann Arbor, MI 48109, USA. alexei@umich.edu
authors.forename: Alexei V
authors.initials: AV
authors.lastname: Tkachenko
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D008846:Micromanipulation / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010812:Physical Stimulation / Q000379:methods; D013314:Stress, Mechanical
chemical_list: D004247:DNA