title: Interconversion between three overstretched DNA structures.
abstract: Double-stranded DNA can exist in multiple structures, including three recently identified overstretched structures (peeled ssDNA, DNA bubble, and S-DNA) for torsion-unconstrained DNA under large tension. Here, we report systematic studies of interconversion between these overstretched DNA structures induced by changing NaCl concentration at constant force. At forces above 70 pN where DNA exists in one of the overstretched states, direct interconversions between S-DNA and DNA bubble for the end-closed DNA construct, as well as interconversions between S-DNA and peeled ssDNA for the end-opened DNA construct, were observed to involve stepwise extension changes. Interestingly, compared to other conversions, the conversion from peeled ssDNA to S-DNA has ultraslow kinetics, which can be explained by formation of secondary hairpin structures on a relaxed strand of peeled ssDNA. Our findings provide important insights into the structures of torsion-unconstrained DNA under large force.
authors.affiliation: BioSystems and Micromechanics, Singapore-MIT Alliance for Research and Technology , Singapore 138602, Singapore.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Zhang
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Qu
authors.forename: Hu
authors.initials: H
authors.lastname: Chen
authors.forename: Ioulia
authors.initials: I
authors.lastname: Rouzina
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
authors.forename: Jie
authors.initials: J
authors.lastname: Yan
mesh_terms: D059371:DNA, B-Form / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004305:Dose-Response Relationship, Drug; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000187:drug effects; D012965:Sodium Chloride / Q000494:pharmacology; D013696:Temperature
chemical_list: D059371:DNA, B-Form; D004277:DNA, Single-Stranded; D012965:Sodium Chloride