Nucleic Acid-Metal Ion Interactions (Rsc Biomolecular Sciences) - Hardcover

Hardcover

ISBN 10: 0854041958 ISBN 13: 9780854041954

Verlag: Royal Society of Chemistry, 2008

Inhaltsangabe

This book provides a perspective of nucleic acid-metal ion interactions with an emphasis on experimental biophysical studies. Topics covered range from x-ray crystallographic studies of transition metal ion coordination by the nucleotide bases to the application of polyelectrolyte theory for understanding the nature of delocalized counterions that surround nucleic acids in solution. Separate chapters cover how nucleic acid-metal ions play a role in the kinetics and thermodynamics of RNA folding, as well as the role of metal ions in RNA catalysis, in disease and in medicine. The book will serve as a reference source for researchers in nucleic acids biophysics and molecular biology, but it also includes enough background material for students and researchers who have not previously worked in the field.

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Über die Autorin bzw. den Autor

Nicholas V Hud is at the Georgia Institute of Technology, Atlanta, USA and has over a decade of research in the area of nucleic acid-cation interactions.

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The quest to understand how nucleic acids function at the most fundamental level requires a detailed understanding of nucleic acid-metal ion interactions, as RNA and DNA are polyanions, their structures depend strongly on their association with metal ions. While scientists have appreciated the intimate connection between metal ions and nucleic acid function for decades, the noncovalent, dynamic nature of these interactions makes their accurate, quantitative description a challenge. Over the past few years, the simultaneous development of solution-state spectroscopic techniques and achievement of high resolution X-ray crystal structures has provided tremendous insight into nucleic acid-metal ion interactions. This insight includes direct evidence for the importance of such interactions in determining nucleic acid structure over orders of magnitude in scale, from the folding pathways of large RNAs to the subtle modulation of DNA groove width. Nucleic Acid-Metal Ion Interactions provides a comprehensive review of the experimental studies that define our current understanding of the subject, with a particular emphasis on biophysical studies. The book is not merely a current review of the literature, however, as the authors also present original material and fresh perspectives. The topics covered range from crystallographic studies of transition metal coordination by single nucleotides, to the application of polyelectrolyte theory in describing the delocalized counterions that surround nucleic acids in solution. Separate chapters describe how nucleic acid-metal interactions modulate both the kinetics and thermodynamics of RNA folding, play important roles in RNA catalysis, and how these interactions are even informing the design of new therapeutics. The book is sufficiently detailed to serve as a reference for researchers active in nucleic acids biophysics or molecular biology. Additionally, chapter authors have supplied sufficient introductory and background material to make this book an accessible first resource for students and researchers who are just beginning to explore this dynamic field.

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Nucleic Acid–Metal Ion Interactions

By Nicholas V. Hud

The Royal Society of Chemistry

Copyright © 2009 Royal Society of Chemistry
All rights reserved.

ISBN: 978-0-85404-195-4

Contents

Chapter 1 Complexes of Nucleic Acids with Group I and II Cations Chiaolong Hsiao, Emmanuel Tannenbaum, Halena VanDeusen, Eli Hershkovitz, Ginger Perng, Allen R. Tannenbaum and Loren Dean Williams, 
Chapter 2 Coordinative Bond Formation Between Metal Ions and Nucleic Acid Bases Bernhard Lippert, 
Chapter 3 Sequence-specific DNA–Metal Ion Interactions Nicholas V. Hud and Aaron E. Engelhart, 
Chapter 4 Metal Ion Interactions with G-Quadruplex Structures Aaron E. Engelhart, Janez Plavec, Özgül Persil and Nicholas V. Hud, 
Chapter 5 Characterization of Nucleic Acid–Metal Ion Binding by Spectroscopic Techniques Victoria J. DeRose, 
Chapter 6 Metal Ions and the Thermodynamics of RNA Folding David P. Giedroc and Nicholas E. Grossoehme, 
Chapter 7 Metal Ions and RNA Folding Kinetics Somdeb Mitra and Michael Brenowitz, 
Chapter 8 Metal Ions in RNA Catalysis John K. Frederiksen, Robert Fong and Joseph A. Piccirilli, 
Chapter 9 Polyanion Models of Nucleic Acid–Metal Ion Interactions J. Michael Schurr, 
Chapter 10 Metal Ion–Nucleic Acid Interactions in Disease and Medicine Ana M. Pizarro and Peter J. Sadler, 
Subject Index, 417, 

CHAPTER 1

Complexes of Nucleic Acids with Group I and II Cations

CHIAOLONG HSIAO, EMMANUEL TANNENBAUM, HALENA VanDEUSEN, ELI HERSHKOVITZ, GINGER PERNG, ALLEN R. TANNENBAUM AND LOREN DEAN WILLIAMS

1.1 Introduction

Recent structures of large RNAs, such as the P4–P6 domain of the Tetra -hymena ribozyme, and larger RNAs such as rRNAs, combined with a general increase over time in the sophistication of diffraction experiments, show cations in diverse and sometimes unexpected environments. The interactions of nucleic acids with cations follow basic principles of coordination chemistry. The effects of cations on RNA stability and conformation demonstrate the endurance of these relatively simple principles.

One focus of this chapter is the coordination of Na+, K+, Ca2+ and Mg2+ by phosphates and nucleic acids. We describe coordination chemistry, electrostatic forces/energetics, conformational effects and ion-selective binding. We explain the origins of the specific requirement for Mg2+ in RNA folding and the tight coupling between Mg2+ binding and RNA conformation. We deconstruct the two binding-mode formalism. We describe crystallographic methods for determining cation positions. We propose a model of RNA folding that is consistent with Mg2+ coordination properties of RNA. Previous reviews are available on roles of metals in biology, in polyelectrolyte theory (see Chapter 9), in DNA structure (see Chapter 3), in RNA folding (see Chapters 6 and 7) and in RNA catalysis (see Chapter 8).

1.1.1 Modern Treasure Troves of Structural Information: Large RNAs

Very large RNA assemblies are now available at high resolution. The largest and most accurate structures are used here in conjunction with smaller structures, down to the level of mononucleotides, to illustrate patterns of interaction of nucleic acids with cations. 23S-rRNAHM refers to the 23S rRNA from the archaeon H. marismortui (2.4 Å resolution, PDB entry 1JJ2), a halophile from the Dead Sea. 23S-rRNATT refers to the 23S rRNA from the eubacterium T. thermophilus (2.8 Å resolution, PDB entry 2J01), isolated from a thermal vent. The fractional sequence identity of the 23S rRNAs from HM and TT is around 60%. RNAP4–P6 refers the 160 nucleotide domain of the self-splicing Tetrahymena thermophila intron (2.3 Å resolution, PDB entry 1HR2, this ΔC209 mutant gives the best available resolution).

1.2 Nucleic Acid Folding

1.2.1 Cations

During protein folding, water molecules in contact with hydrophobic surfaces are released to bulk solvent. During nucleic acid folding, cations are sequestered from bulk solvent and held in close proximity to the polymer. Protein side-chains are multifarious, with a variety of shapes and chemical properties. The nucleic acid backbone is intricate, with many accessible rotameric states, and carries charge.

Functional nucleic acids generally fold into compact and stable states of given conformation. DNA can form quadruplexes, triplexes, i-motifs, etc. Structured RNAs range in size from aptamers and tRNAs to ribosomes. However some functional nucleic acids, such as riboswitches, are conformationally polymorphic. For our purposes, folded nucleic acid structures fall into three general classes: (i) helical structures such as A-form, B-form and triplexes, (ii) quasi-globular structures such as tRNA, with base–base tertiary interactions but no buried phosphates, and quadruplexes, and (iii) true globular structures such as the Tetrahymena ribozyme and its P4–P6 domain, with base–base tertiary interactions plus buried OP atoms (OP indicates a non-bridging phosphate oxygen). True globular structures have distinct 'insides' and 'outsides'. Folding of helices, quasi-globular structures and true globular structures increases proximities of phosphate groups and the electrostatic repulsion among them. Therefore, folding is intrinsically linked to association with cations. Phosphate-phosphate repulsion must be offset by attraction between phosphates and cations. Cations most strongly associate with regions of DNA and RNA in which phosphate groups assume greatest 'density'.

As will become clear in the following sections, Mg2+ stabilizes distinctive conformational and energetic states of nucleic acids. Mg2+ shares a special geometric and electrostatic complementarity with phosphate, with a specific coordination and thermodynamic fingerprint. These states are simply not accessible in the absence of Mg2+ (or Mn2+), even when other cations are at high concentration. The thermodynamic and conformational consequences of first-shell OP interactions with Mg2+ are different to those for neutral ligands or for other cations, with lesser charge or greater size.

1.2.2 The RNA Folding Hierarchy

RNA folding is hierarchical. Folding progresses through a series of intermediates that are commonly characterized by extents and types of base–base hydrogen bonding and stacking interactions. The unfolded state, the random coil, is a conformationally polymorphic and fluctuating ensemble with few local or long-range base–base interactions. Early intermediates contain double-stranded stems and hairpin loops, interspersed by single-stranded regions. These stems and loops are known collectively as secondary structural units. Late intermediates and the final folded state are stabilized by base–base tertiary interactions, between residues that are remote in the secondary structure. To a first approximation, secondary structure can be conceptually and experimentally separated from tertiary structure. Secondary structure forms before tertiary structure and is favorable in a broad range of ionic conditions. Tertiary structure is favored by divalent cations. Although compact structures with base–base tertiary interactions can be achieved at very high concentrations of other cations, for true globular structures, the fully folded state is absolutely dependent on Mg2+. It can be useful to make a distinction between the tertiary structure of an RNA, which is a description of short- and-long range...

Details zur Ausgabe

• Verlag: Royal Society of Chemistry
• Erscheinungsdatum: 2008
• Sprache: Englisch
• ISBN 10: 0854041958
• ISBN 13: 9780854041954
• Einband: Gebundene Ausgabe
• Anzahl der Seiten: 433
• Herausgeber: Hud Nicholas V
• Kontakt zum Hersteller: Nicht verfügbar
• Verantwortliche Person: gpsr@libri.de; gpsr@libri.de; ; Friedensallee 273; Hamburg; 22763; Deutschland