title: Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.
abstract: Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts. Here, we use a battery of nuclear magnetic resonance techniques to examine how deleting a single bulge residue (C24) from the human immunodeficiency virus type 1 (HIV-1) transactivation response element (TAR) trinucleotide bulge (U23-C24-U25) affects dynamics over a broad range of time scales. Shortening the bulge has an effect on picosecond-to-nanosecond interhelical and local bulge dynamics similar to that casued by increasing the Mg(2+) and Na(+) concentration, whereby a preexisting two-state equilibrium in TAR is shifted away from a bent flexible conformation toward a coaxial conformation, in which all three bulge residues are flipped out and flexible. Surprisingly, the point deletion minimally affects microsecond-to-millisecond conformational exchange directed toward two low-populated and short-lived excited conformational states that form through reshuffling of bases pairs throughout TAR. The mutant does, however, adopt a slightly different excited conformational state on the millisecond time scale, in which U23 is intrahelical, mimicking the expected conformation of residue C24 in the excited conformational state of wild-type TAR. Thus, minor changes in HJH topology preserve motional modes in RNA occurring over the picosecond-to-millisecond time scales but alter the relative populations of the sampled states or cause subtle changes in their conformational features.
authors.affiliation: Department of Chemistry, Duke University , Durham, North Carolina 27708, United States.
authors.forename: Dawn K
authors.initials: DK
authors.lastname: Merriman
authors.affiliation: Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.
authors.forename: Yi
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Baxter Health Care (Suzhou) Company, Ltd. , Suzhou, Jiang Su 215028, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Yang
authors.affiliation: Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.
authors.forename: Isaac J
authors.initials: IJ
authors.lastname: Kimsey
authors.affiliation: Department of Chemistry and Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors.forename: Anisha
authors.initials: A
authors.lastname: Shakya
authors.affiliation: Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.
authors.forename: Mary
authors.initials: M
authors.lastname: Clay
authors.affiliation: Department of Chemistry, Duke University , Durham, North Carolina 27708, United States.|Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.
authors.forename: Hashim M
authors.initials: HM
authors.lastname: Al-Hashimi
mesh_terms: D001483:Base Sequence; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D007700:Kinetics; D008958:Models, Molecular; D009068:Movement; D009154:Mutation; D009690:Nucleic Acid Conformation; D009711:Nucleotides; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D009711:Nucleotides; D012367:RNA, Viral