title: Structure and dynamics of the HIV-1 frameshift element RNA.
abstract: The HIV-1 ribosomal frameshift element is highly structured, regulates translation of all virally encoded enzymes, and is a promising therapeutic target. The prior model for this motif contains two helices separated by a three-nucleotide bulge. Modifications to this model were suggested by SHAPE chemical probing of an entire HIV-1 RNA genome. Novel features of the SHAPE-directed model include alternate helical conformations and a larger, more complex structure. These structural elements also support the presence of a secondary frameshift site within the frameshift domain. Here, we use oligonucleotide-directed structure perturbation, probing in the presence of formamide, and in-virion experiments to examine these models. Our data support a model in which the frameshift domain is anchored by a stable helix outside the conventional domain. Less stable helices within the domain can switch from the SHAPE-predicted to the two-helix conformation. Translational frameshifting assays with frameshift domain mutants support a functional role for the interactions predicted by and specific to the SHAPE-directed model. These results reveal that the HIV-1 frameshift domain is a complex, dynamic structure and underscore the importance of analyzing folding in the context of full-length RNAs.
authors.affiliation: Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599-3290, United States.
authors.forename: Justin T
authors.initials: JT
authors.lastname: Low
authors.forename: Pablo
authors.initials: P
authors.lastname: Garcia-Miranda
authors.forename: Kathryn D
authors.initials: KD
authors.lastname: Mouzakis
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Gorelick
authors.forename: Samuel E
authors.initials: SE
authors.lastname: Butcher
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Weeks
mesh_terms: D018965:Frameshifting, Ribosomal; D015497:HIV-1 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D012367:RNA, Viral