title: Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.
abstract: The structure of a new form of duplex DNA, the antiparallel Hoogsteen duplex, is studied in polyd(AT) sequences by means of state-of-the-art molecular dynamics simulations in aqueous solution. The structure, which was found to be stable in all of the simulations, has many similarities with the standard Watson-Crick duplex in terms of general structure, flexibility, and molecular recognition patterns. Accurate MM-PB/SA (and MM-GB/SA) analysis shows that the new structure has an effective energy similar to that of the B-type duplex, while it is slightly disfavored by intramolecular entropic considerations. Overall, MD simulations strongly suggest that the antiparallel Hoogsteen duplex is an accessible structure for a polyd(AT) sequence, which might compete under proper experimental conditions with normal B-DNA. MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved.
authors: Molecular Modeling & Bioinformatic Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors: Elena
authors: E
authors: Cubero
authors: Nicola G A
authors: NG
authors: Abrescia
authors: Juan A
authors: JA
authors: Subirana
authors: F Javier
authors: FJ
authors: Luque
authors: Modesto
authors: M
authors: Orozco
mesh_terms: D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011067:Poly dA-dT / Q000737:chemistry*; D012996:Solutions; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D012996:Solutions; D014867:Water; D011067:Poly dA-dT; D004247:DNA