title: A computational approach to the mechanism of self-cleavage of hammerhead RNA.
abstract: Extensive minimization and dynamics computational studies of the hammerhead structural domain of the virusoid of lucerne transient streak virus have been carried out. The following observations at the self-cleavage position are derived from the resulting three-dimensional structure: (i) the cytosine base is at the surface and does not interact with another base (it is free to move), and (ii) the ribose-phosphate backbone is forced to take an abrupt turn since it bridges stems I and III, and this turn points the pro-S and pro-R oxygens of the phosphate to the inward side of the hammerhead. These structural features are independent of the hammerhead being open or closed and allow an unencumbered 3'- to 2'-endo conformational change of the ribose with the resultant creation of an unusual stereochemistry that allows a direct in-line self-cleavage reaction. In the closed hammerhead structure, interactions of stems I and II create a vacancy into which the catalytic hydrated Mg(II) may be docked on labile phosphate. This opening is not present if stems I and II are shortened.
authors.affiliation: Department of Chemistry, University of California, Santa Barbara 93106.
authors.forename: H Y
authors.initials: HY
authors.lastname: Mei
authors.forename: T W
authors.initials: TW
authors.lastname: Kaaret
authors.forename: T C
authors.initials: TC
authors.lastname: Bruice
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010942:Plant Viruses / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*
chemical_list: D012367:RNA, Viral; D008274:Magnesium