Regular Article
RNA Structure and Stability

https://doi.org/10.1006/smvy.1997.0118Get rights and content

Abstract

RNA molecules fold into specific base-paired conformations that contain single-stranded regions, A-form double helices, hairpin loops, internal loops, bulges, junctions, pseudoknots, kissing hairpins, and so forth. These structural motifs are recognized by proteins, other RNAs, and other parts of the same RNA. The interactions of these structural elements are crucial to the biological functions of the RNA molecules. We describe the different motifs and discuss their thermodynamic stabilities relative to single strands of RNA. The stabilities determine under what conditions they occur and whether they change when interacting with proteins or other ligands.

References (70)

  • J.D. Puglisi et al.

    Conformation of an RNA pseudoknot

    J. Mol. Biol.

    (1990)
  • L.X. Shen et al.

    The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus

    J. Mol. Biol.

    (1995)
  • H. Kang et al.

    Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus

    J. Mol. Biol.

    (1996)
  • X. Chen et al.

    A characteristic bent conformation of RNA pseudoknots causes minus-one frameshifting during translation of retroviral RNA

    J. Mol. Biol.

    (1996)
  • P.F. Predki et al.

    Dissecting RNA–protein interactions: RNA–RNA recognition by Rop

    Cell

    (1995)
  • L. Jaeger et al.

    Involvement of a GNRA tetraloop in long-range RNA tertiary interactions

    J. Mol. Biol.

    (1994)
  • P.N. Borer et al.

    Stability of ribonucleic acid double-stranded helices

    J. Mol. Biol.

    (1974)
  • W. Saenger

    Principles of Nucleic Acid Structure

    (1984)
  • F.U. Gast et al.

    Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: evidence that A-tracts do not generate curvature in RNA

    Biochemistry

    (1991)
  • K.M. Weeks et al.

    Major groove accessibility of RNA

    Science

    (1993)
  • P.N. Borer et al.

    Proton NMR and structural features of a 24-nucleotide RNA hairpin

    Biochemistry

    (1995)
  • Y.T. van den Hoogen et al.

    Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG)(CCGCCCAG) A model-building and NMR study

    Nucleic Acids Res.

    (1988)
  • K.J. Luebke et al.

    Sequence effects on RNA bulge-induced helix bending and a conserved five-nucleotide bulge from the group I introns

    Biochemistry

    (1996)
  • M. Zacharias et al.

    The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide

    Proc. Natl. Acad. Sci. USA

    (1995)
  • J.D. Puglisi et al.

    Conformation of the TAR RNA–arginine complex by NMR spectroscopy

    Science

    (1992)
  • R.F. Gesteland et al.

    The RNA World

    (1993)
  • B. Wimberly et al.

    The conformation of loop E of eukaryotic 5S ribosomal RNA

    Biochemistry

    (1993)
  • Z. Cai et al.

    Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite

    Biochemistry

    (1996)
  • T. Dieckmann et al.

    Solution structure of an ATP-binding RNA aptamer reveals a novel fold

    RNA

    (1996)
  • S.R. Holbrook et al.

    Crystal structure of an RNA double helix incorporating a track of non-Watson–Crick base pairs

    Nature

    (1991)
  • J. SantaLucia et al.

    Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics

    Biochemistry

    (1993)
  • R.S. Tang et al.

    Bend and helical twist associated with a symmetric internal loop from 5S ribosomal RNA

    Biochemistry

    (1994)
  • J.L. Battiste et al.

    Alpha helix–RNA major groove recognition in an HIV-1 rev peptide–RRE RNA complex

    Science

    (1996)
  • D. Fourmy et al.

    Structure of the A Site ofEscherichia coli

    Science

    (1996)
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