Principles of nucleic acid structure /

Principles of nucleic acid structure /

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Bibliographic Details
Author / Creator:Neidle, Stephen.
Edition:First edition.
Imprint:Amsterdam : Elsevier ; Boston : Academic Press, 2008.
Description:xii, 289 p. : ill. ; 26 cm.
Language:English
Subject:
Nucleic acids.
Nucleic Acid Conformation.
Nucleic Acids -- chemistry.
Nucleic acids.
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/6659562
Hidden Bibliographic Details
ISBN:9780123695079 (pbk.)
0123695074 (pbk.)
Notes:Includes bibliographical references and index.
Other form:Online version: Neidle, Stephen. Principles of nucleic acid structure. First edition. Amsterdam : Elsevier ; Boston : Academic Press, 2008
Table of Contents:
  • 1. Methods for Studying Nucleic Acid Structure
  • 1.1. Introduction
  • 1.2. X-ray Diffraction Methods for Structural Analysis
  • 1.2.1. Overview
  • 1.2.2. Fiber Diffraction Methods
  • 1.2.3. Single-Crystal Methods
  • 1.3. NMR Methods for Studying Nucleic Acid Structure and Dynamics
  • 1.4. Molecular Modelling and Simulation of Nucleic Acids
  • 1.5. Chemical, Enzymatic, and Biophysical Probes of Structure and Dynamics
  • 1.6. Sources of Structural Data
  • 1.7. Visualization of Nucleic Acid Molecular Structures
  • 1.7.1. The Structures in This Book
  • 2. The Building-Blocks of DNA and RNA
  • 2.1. Introduction
  • 2.2. Base Pairing
  • 2.3. Base and Base Pair Flexibility
  • 2.4. Sugar Puckers
  • 2.5. Conformations About the Glycosidic Bond
  • 2.6. The Backbone Torsion Angles and Correlated Flexibility
  • 3. DNA Structure as Observed in Fibers and Crystals
  • 3.1. Structural Fundamentals
  • 3.1.1. Helical Parameters
  • 3.1.2. Base-Pair Morphological Features
  • 3.2. Polynucleotide Structures from Fiber Diffraction Studies
  • 3.2.1. Classic DNA Structures
  • 3.2.2. DNA Polymorphism in Fibers
  • 3.3. B-DNA Oligonucleotide Structure as Seen in Crystallographic Analyses
  • 3.3.1. The Dickerson-Drew Dodecamer
  • 3.3.2. Other Studies of the Dickerson-Drew Dodecamer
  • 3.3.3. Other B-DNA Oligonucleotide Structures
  • 3.3.4. Sequence-Dependent Features of B-DNA: Their Occurrence and Their Prediction
  • 3.4. A-DNA Oligonucleotide Crystal Structures
  • 3.4.1. A-Form Octanucleotides
  • 3.4.2. Do A-Form Oligonucleotides Occur in Solution? Crystal-Packing Effects
  • 3.4.3. The A [left and right arrow] B Transition in Crystals
  • 3.5. Z-DNA - Left-Handed DNA
  • 3.5.1. The Z'DNA Hexanucleotide Crystal Structure
  • 3.5.2. Overall Structural Features
  • 3.5.3. The Z-DNA Helix
  • 3.5.4. Other Z-DNA Structures
  • 3.5.5. Biological Aspects of Z-DNA
  • 3.6. Bent DNA
  • 3.6.1. DNA Periodicity in Solution
  • 3.6.2. A-Tracts and Bending
  • 3.6.3. Structures Showing Bending
  • 3.6.4. The Structure of Poly dA[middot]dT
  • 3.7. Concluding Remarks
  • 4. Nonstandard and Higher-Order DNA Structures: DNA-DNA Recognition
  • 4.1. Mismatches in DNA
  • 4.1.1. General Features
  • 4.1.2. Purine: Purine Mismatches
  • 4.1.3. Alkylation Mismatches
  • 4.2. DNA Triple Helices
  • 4.2.1. Introduction
  • 4.2.2. Structural Studies
  • 4.2.3. Antiparallel Triplexes and Nonstandard Base-pairings
  • 4.2.4. Triplex Applications
  • 4.3. Guanine Quadruplexes
  • 4.3.1. Introduction
  • 4.3.2. Overall Structural Features of Quadruplex DNA
  • 4.3.3. Examples of Simple Quadruplex Structures
  • 4.3.4. Some Complex Quadruplex Structures
  • 4.3.5. The i-Motif
  • 4.4. DNA Junctions
  • 4.4.1. Holliday Junction Structures
  • 4.4.2. DNA Enzyme Structures
  • 4.5. Unnatural DNA Structures
  • 5. Principles of Small Molecule-DNA Recognition
  • 5.1. Introduction
  • 5.2. DNA-Water Interactions
  • 5.2.1. Hydration in the Grooves in Detail
  • 5.3. General Features of DNA-Drug and Small-Molecule Recognition
  • 5.4. Intercalative Binding
  • 5.4.1. Simple Intercalators
  • 5.4.2. Complex Intercalators
  • 5.4.3. Major-Groove Intercalation
  • 5.4.4. Bis-Intercalators
  • 5.5. Intercalative-Type Binding to Higher-Order DNAs
  • 5.5.1. Triplex DNA-Ligand Interactions
  • 5.5.2. Ligand Binding to Quadruplex DNAs
  • 5.5.3. Ligand Binding to Junction DNAs
  • 5.6. Groove-Binding Molecules
  • 5.6.1. Simple Groove Binding Molecules
  • 5.6.2. Netropsin and Distamycin
  • 5.6.3. Sequence-Specific Polyamides
  • 5.7. Small Molecule Covalent Bonding to DNA
  • 5.7.1. The Platinum Drugs
  • 5.7.2. Covalent-Binding Combined with Sequence-Specific Recognition
  • 6. RNA Structures and Their Diversity
  • 6.1. Introduction
  • 6.2. Fundamentals of RNA Structure
  • 6.2.1. Helical RNA Conformations
  • 6.2.2. Mismatched and Bulged RNA Structures
  • 6.3. Transfer RNA Structures
  • 6.4. Ribozymes
  • 6.4.1. The Hammerhead Ribozyme
  • 6.4.2. Complex Ribozymes
  • 6.5. Riboswitches
  • 6.6. The Ribosome, a Ribozyme Machine
  • 6.6.1. The Structure of the 30S Subunit
  • 6.6.2. The Structure of the 50S subunit
  • 6.6.3. Complete Ribosome Structures
  • 6.7. RNA-Drug Complexes
  • 6.8. RNA Motifs
  • 7. Principles of Protein-DNA Recognition
  • 7.1. Introduction
  • 7.2. Direct Protein-DNA Contacts
  • 7.3. Major-Groove Interactions - the [alpha]-Helix as the Recognition Element
  • 7.4. Zinc-Finger Recognition Modes
  • 7.5. Other Major Groove Recognition Motifs
  • 7.6. Minor-Groove Recognition
  • 7.6.1. Recognition of B-DNA
  • 7.6.2. The Opening-up of the Minor Groove by TBP
  • 7.6.3. Other Proteins that Induce Bending of DNA
  • 7.7. DNA-Bending and Protein Recognition
  • 7.8. Protein-DNA-Smail Molecule Recognition
  • Index
Purchased by the George E. & Mable L. Kaufmann Book Fund bookplate
The John Crerar Library bookplate

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