Non-Protein Coding RNAs

1. Front Matter

   Pages i-xi

   PDF

2. RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

   • Lorena Nasalean, Jesse Stombaugh, Craig L. Zirbel, Neocles B. Leontis

   Pages 1-26

3. Theory of RNA Folding: From Hairpins to Ribozymes

   • D. Thirumalai, Changbong Hyeon

   Pages 27-47

4. Thermodynamics and Kinetics of RNA Unfolding and Refolding

   • Pan T. X. Li, Ignacio Tinoco Jr.

   Pages 49-72

5. Ribozyme Catalysis of Phosphodiester Bond Isomerization: The Hammerhead RNA and Its Relatives

   • William G. Scott

   Pages 73-102

6. The Small Ribozymes: Common and Diverse Features Observed Through the FRET Lens

   • Nils G. Walter, Shiamalee Perumal

   Pages 103-127

7. Structure and Mechanism of the glmS Ribozyme

   • Juliane K. Soukup, Garrett A. Soukup

   Pages 129-143

8. Group I Ribozymes as a Paradigm for RNA Folding and Evolution

   • Sarah A. Woodson, Seema Chauhan

   Pages 145-166

9. Group II Introns and Their Protein Collaborators

   • Amanda Solem, Nora Zingler, Anna Marie Pyle, Jennifer Li- Pook-Than

   Pages 167-182

10. Understanding the Role of Metal Ions in RNA Folding and Function: Lessons from RNase P, a Ribonucleoprotein Enzyme

    • Michael E. Harris, Eric L. Christian

    Pages 183-213

11. Beyond Crystallography: Investigating the Conformational Dynamics of the Purine Riboswitch

    • Colby D. Stoddard, Robert T. Batey

    Pages 215-228

12. Ligand Binding and Conformational Changes in the Purine-Binding Riboswitch Aptamer Domains

    • Jonas Noeske, Janina Buck, Jens Wöhnert, Harald Schwalbe

    Pages 229-247

13. The RNA–Protein Complexes of E. coli Hfq: Form and Function

    • Taewoo Lee, Andrew L. Feig

    Pages 249-271

14. Assembly of the Human Signal Recognition Particle

    • Elena Menichelli, Kiyoshi Nagai

    Pages 273-284

15. Forms and Functions of Telomerase RNA

    • Kathleen Collins

    Pages 285-301

16. Ribosomal Dynamics: Intrinsic Instability of a Molecular Machine

    • Haixiao Gao, Jamie Le Barron, Joachim Frank

    Pages 303-316

17. Biophysical Analyses of IRES RNAs from the Dicistroviridae: Linking Architecture to Function

    • Jeffrey S. Kief

    Pages 317-333

18. Structure and Gene-Silencing Mechanisms of Small Noncoding RNAs

    • Chia-Ying Chu, Tariq M. Rana

    Pages 335-356

19. Back Matter

    Pages 357-398

    PDF

The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.

• Einzelmolekülmikroskopie
• FRET
• Kernspinresonanz
• Nuclear Magnetic Resonance
• Riboswitch RNA
• Röntgenstrukturanalyse
• Single Molecule Microscopy
• X-ray
• X-ray crystallography
• electron microscopy
• enzymes
• gene expression
• microscopy
• physiology
• thermodynamics

• Department of Chemistry, University of Michigan, Ann Arbor, USA

  Nils G. Walter

• Department of Biophysics, Johns Hopkins University, Baltimore, USA

  Sarah A. Woodson

• Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, USA

  Robert T. Batey

Policies and ethics