title: Structure, recognition properties, and flexibility of the DNA.RNA hybrid.
abstract: Molecular dynamics is used to investigate the properties of the DNA.RNA hybrid in aqueous solution at room temperature. The structure of the hybrid is intermediate between A and B forms but, in general, closer to the canonical A-type helix. All the riboses exhibit North puckerings, while 2'-deoxyriboses exist in North, East, and South puckerings, the latter being the most populated one. The molecular recognition pattern of the DNA.RNA hybrid is a unique combination of those of normal DNA and RNA duplexes. Finally, the results obtained from essential dynamics and stiffness analysis demonstrate the large and very asymmetric flexibility of the hybrid and the strong predilection that each strand (DNA or RNA) has on the nature of their intrinsic motions in the corresponding homoduplexes. The implications of the unique structural and dynamic properties of the DNA.RNA hybrid on the mechanism of cleavage by RNase H are discussed.
authors.affiliation: Molecular Modeling and Bioinformatics Unit, Parc Cientific de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Agnes
authors.initials: A
authors.lastname: Noy
authors.forename: Alberto
authors.initials: A
authors.lastname: Pérez
authors.forename: Manuel
authors.initials: M
authors.lastname: Márquez
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016914:Ribonuclease H / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D012313:RNA; D004247:DNA; D016914:Ribonuclease H