title: Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse.
abstract: We explore the use of a fast laser melting simulation approach combined with atomistic molecular dynamics simulations in order to determine the melting and healing responses of B-DNA and Z-DNA dodecamers with the same d(5'-CGCGCGCGCGCG-3')2 sequence. The frequency of the laser pulse is specifically tuned to disrupt Watson-Crick hydrogen bonds, thus inducing melting of the DNA duplexes. Subsequently, the structures relax and partially refold, depending on the field strength. In addition to the inherent interest of the nonequilibrium melting process, we propose that fast melting by an infrared laser pulse could be used as a technique for a fast comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. This could be particularly useful for nonstandard secondary structures involving non-canonical base pairs, mismatches, etc.
authors.affiliation: Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors.forename: Viet Hoang
authors.initials: VH
authors.lastname: Man
authors.affiliation: Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Pan
authors.affiliation: Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors.forename: Celeste
authors.initials: C
authors.lastname: Sagui
authors.affiliation: Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Roland
mesh_terms: D059371:DNA, B-Form / Q000737:chemistry*; D043542:DNA, Z-Form / Q000737:chemistry*; D007834:Lasers; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D059371:DNA, B-Form; D043542:DNA, Z-Form