title: Effects of the eye phase in DNA unzipping.
abstract: The onset of the "eye phase" (a phase consisting of configurations of eye-type conformations or bubbles in the double-stranded DNA) and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "sawtooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.
authors.affiliation: Physics Section, MMV, Banaras Hindu University, Varanasi 221 005, India.
authors.forename: Debaprasad
authors.initials: D
authors.lastname: Giri
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kumar
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D044367:Phase Transition
chemical_list: D004247:DNA