title: Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.
abstract: A series of d (AT)(n) oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation.
authors.affiliation: Molecular Modelling & Bioinformatic Unit, Institut de Recerca Biomèdica-Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: Cubero
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded; D019277:Entropy; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry; D017433:Protein Structure, Secondary; D011993:Recombinant Fusion Proteins / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D011993:Recombinant Fusion Proteins; D004247:DNA