Structure and Dynamics of RNA

1. Front Matter

   Pages i-ix

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2. Improved Parameters for Prediction of RNA Secondary Structure and Insights into why RNA forms Double Helixes

   • D. H. Turner, S. M. Freier, N. Sugimoto, D. R. Hickey, J. A. Jaeger, A. Sinclair et al.

   Pages 1-13

3. Anomalous Conformations of RNA Constituents : 2D NMR and Calculational Studies

   • Cornelis Altona

   Pages 15-30

4. NMR Studies of Base-Pair Kinetics of Nucleic Acids

   • Jean Louis Leroy, Daniel Broseta, Nicolas Bolo, Maurice Guéron

   Pages 31-44

5. Picosecond Time Domain Spectroscopy of Structure and Dynamics in Nucleic Acids

   • Rudolf Rigler, Flora Claesens

   Pages 45-54

6. Z-RNA: A Left-Handed Double Helix

   • Ignacio Tinoco Jr., Phillip Cruz, Peter Davis, Kathleen Hall, Charles C. Hardin, Richard A. Mathies et al.

   Pages 55-68

7. A Better Way to Make RNA for Physical Studies

   • P. Lowary, J. Sampson, J. Milligan, D. Groebe, O. C. Uhlenbeck

   Pages 69-76

8. Mg2+ — Inner Sphere Complexes at “Ends” and “Bends” of Polynucleotides and their Potential Role as Long Range Inducers of Conformation Changes

   • Dietmar Porschke

   Pages 77-85

9. Pseudoknots in RNA: A Novel Folding Principle

   • Cornelis W. A. Pleij, Alex van Belkum, Krijn Rietveld, L. Bosch

   Pages 87-98

10. Proton NMR Studies of RNA’S and Related Enzymes Using Isotope Labels

    • A. G. Redfield, B.-S. Choi, R. H. Griffey, M. Jarema, P. Rosevear, P. Hoben et al.

    Pages 99-112

11. GU Base Pairs and Variable Loop in Yeast tRNAAsp

    • D. Moras, P. Dumas, E. Westhof

    Pages 113-124

12. Correlation Between Crystal and Solution Structures in tRNA. Yeast tRNAPhe and tRNAAsp the Models for Free and Messenger RNA Bound tRNAs

    • Richard Giegé, Anne-Catherine Dock, Philippe Dumas, Jean-Pierre Ebel, Pascale Romby, Eric Westhof et al.

    Pages 125-136

13. The Solution Structures of RNA Fragments Determined by Nuclear Overhauser Enhancement Measurements

    • A. M. Gronenborn, G. M. Clore

    Pages 137-149

14. Molecular Dynamics Simulation of the Anticodon Arm of Phenylalanine Transfer RNA

    • Lennart Nilsson, Martin Karplus

    Pages 151-159

15. Anticodon-Anticodon Interactions and tRNA Sequence Comparison: Approaches to Codon Recognition

    • H. Grosjean, C. Houssier, R. Cedergren

    Pages 161-174

16. Studies on 15N Labelled 5S RNA: Assignments in the Helix V Region of 5S RNA, and in the 5S/L25 Complex

    • M. Jarema, P. B. Moore

    Pages 175-189

17. Equilibria in Ribosomal RNA Secondary Structure

    • Rupert De Wachter

    Pages 191-204

18. A Comparative Analysis of Structural Dynamics in 5S rRNA

    • Martin Digweed, Tomas Pieler, Volker A. Erdmann

    Pages 205-219

19. A Domain of 23S Ribosomal RNA in Search of a Function

    • Asser Andersen, Niels Larsen, Henrik Leffers, Jørgen Kjems, Roger Garrett

    Pages 221-237

20. The Three-Dimensional Organization of Escherichia Coli Ribosomal RNA

    • Richard Brimacombe

    Pages 239-251

This volume contains contributions from the speakers at the NATO Advanced Research Workshop on "3D 5tructure and Dynamics of RNA", which was held in Renesse, The Netherlands, 21 - 24 August, 1985. Two major developments have determined the progress of nucleic acid research during the last decade. First, manipulation of genetic material by recombinant DNA methodology has enabled detailed studies of the function of nucleic acids in vivo. 5econd, the use of powerful physical methods, such as X-ray diffraction and nuclear magnetic resonance spectroscopy, in the study of biomacromolecules has provided information regarding the structure and the dynamics of nucleic acids. Both developments were enabled by the advance of synthetic methods that allow preparation of nucleic acid molecules of required sequence and length. The basic understanding of nucleic acid function will ultimately depend on a close collaboration between molecular biologists and biophy­ sicists. In the case of RNA, the ground rules for the formation of secondary structure have been derived from physical studies of oligoribonucleotides. Powerfull spectroscopic techniques have revealed more details of ~~A structure including novel conformations (e.g. left-handed Z-RNA). A wealth of information has been obtained by studying the relatively small transfer RNA molecules. A few of these RNAs have been crystallized, enabling determination of their three-dimensional structure. It has become apparent that "non-classical" basepairing between distal nucleotides gives rise to tertiary interactions, determining the overall shape of the molecule.

• DNA
• X-ray
• acid
• development
• diffraction
• dynamics
• information
• kinetics
• magnetic resonance
• magnetic resonance spectroscopy
• nuclear magnetic resonance
• research
• resonance
• structural dynamics
• structure

• University of Leiden, Leiden, The Netherlands

  P. H. Knippenberg

• University of Nijmegen, Nijmegen, The Netherlands

  C. W. Hilbers

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