Structure, recognition properties, and flexibility of the DNA.RNA hybrid.

TitleStructure, recognition properties, and flexibility of the DNA.RNA hybrid.
Publication TypeJournal Article
Year of Publication2005
AuthorsNoy, Agnes, Pérez Alberto, Márquez Manuel, F Luque Javier, and Orozco Modesto
JournalJ Am Chem Soc
Date Published2005 Apr 6
KeywordsComputer Simulation, Crystallography, DNA, Models, Molecular, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes, Ribonuclease H, RNA, Structure-Activity Relationship, Substrate Specificity, Thermodynamics, X-Ray

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.