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, A, Perez A, Marquez M, Luque FJ, Orozco M
JournalJournal of the American Chemical Society
Pagination4910 - 4920
Date Published2005/04/06/
KeywordsComputer Simulation; Crystallography, Molecular; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes/chemistry/metabolism; RNA/chemistry/metabolism; Ribonuclease H/chemistry/metabolism; Structure-Activity Relationship; Substrate Specificity; Thermodynamics, X-Ray; DNA/chemistry/metabolism; Models
AbstractMolecular 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.