Principles of nucleic acid structure /

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Principles of Nucleic Acid Structure, Second Edition, provides the most complete and concise summary of underlying principles and approaches to studying nucleic acid structure, including discussions of X-ray crystallography, NMR, molecular modelling and databases. The book's focus is on a surve...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Autores principales: Neidle, Stephen (Autor), Sanderson, Mark (Autor)
Formato: Electrónico eBook
Idioma:Inglés
Publicado: London, United Kingdom : Academic Press, 2021.
Edición:Second edition.
Temas:
Nucleic acids > Structure.
Acceso en línea:Texto completo
Tabla de Contenidos:
  • Front Cover
  • PRINCIPLES OF NUCLEIC ACID STRUCTURE
  • PRINCIPLES OF NUCLEIC ACID STRUCTURE
  • Copyright
  • CONTENTS
  • Preface to the second edition
  • Preface from the first edition
  • 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 Fibre diffraction methods
  • 1.2.3 Single-crystal methods
  • 1.3 NMR methods for studying nucleic acid structure and dynamics
  • 1.4 Cryo-EM methods for macromolecular complexes
  • 1.5 Molecular modelling and simulation of nucleic acids
  • 1.6 Chemical, enzymatic and biophysical probes of structure and dynamics
  • 1.7 Sources of structural data
  • 1.8 Visualisation of nucleic acid molecular structures
  • 1.8.1 The structural visualisations in this book
  • References
  • Further reading
  • General
  • The history of DNA structure
  • More detailed accounts of particular topics can be found in the following
  • X-ray crystallography
  • NMR methods
  • Molecular modelling and simulation methods
  • Chemical, enzymatic, biophysical and single-molecule probes of nucleic acid structure
  • The nucleic acid and protein databases
  • 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
  • References
  • Further reading
  • 3
  • DNA structure as observed in fibres and crystals
  • 3.1 Structural fundamentals
  • 3.1.1 Helical parameters
  • 3.1.2 Base-pair morphological features
  • 3.2 Polynucleotide structures from fibre diffraction studies
  • 3.2.1 Classic DNA structures
  • 3.2.2 DNA polymorphism in fibres
  • 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 A₄B 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 dAdT
  • 3.7 Concluding remarks
  • References
  • Further reading
  • 4
  • Non-standard and higher-order DNA structures: DNA-DNA recognition
  • 4.1 Mismatches in DNA
  • 4.1.1 General features
  • 4.1.2 Purine:purine mis-matches
  • 4.1.3 Alkylation mismatches
  • 4.1.4 Alkylation at Watson-Crick base pairs
  • 4.2 DNA triple helices
  • 4.2.1 Introduction
  • 4.2.2 Structural studies
  • 4.2.3 Anti-parallel triplexes and non-standard 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 Telomeric quadruplex structures
  • 4.3.4 Human telomeric quadruplex structures
  • 4.3.5 Promoter and other quadruplexes
  • 4.3.6 Quadruplex-duplex junctions
  • 4.3.7 Left-handed quadruplexes
  • 4.4 The i-motif
  • 4.5 DNA junctions
  • 4.5.1 Holliday junction structures
  • 4.5.2 DNA enzyme structures
  • 4.6 Unnatural DNA structures
  • References
  • Further reading
  • Mispairing
  • Triplexes
  • Telomeres and quadruplexes
  • DNA junctions
  • 5
  • Principles of small molecule-DNA recognition
  • 5.1 Introduction
  • 5.2 DNA-water interactions.
  • 7.6.3 The OB-fold domain
  • 7.6.4 The immunoglobulin fold
  • 7.6.5 B3 domains
  • 7.7 Minor groove recognition
  • 7.7.1 Recognition of B-DNA
  • 7.7.2 The opening-up of the minor groove by TBP
  • 7.7.3 Other proteins that induce bending of DNA
  • 7.8 DNA bending and protein recognition
  • 7.9 Protein-DNA small-molecule recognition
  • 7.10 DNA-binding proteins and their role in genomics
  • 7.10.1 Zinc finger proteins
  • 7.10.2 The development of zinc finger targeting
  • 7.10.3 Repair of DNA lesions by site-specific cutting and DNA recombination
  • 7.10.4 The regulation of gene control by ZFPs
  • 7.10.5 CRISPR-associated nuclease Cas9
  • References
  • Further reading
  • Useful web sites
  • 8
  • RNA binding proteins
  • 8.1 Aminoacyl synthetase-tRNA complexes
  • 8.2 Structure of reverse transcriptases
  • 8.3 snRPs (small nuclear ribonucleoproteins)
  • 8.4 The ribosome
  • 8.4.1 The ribosomal subunits
  • 8.4.1.1 The 30S subunit
  • 8.4.1.2 The 50S subunit
  • 8.4.1.3 The entire 70S ribosomal structure
  • 8.4.2 Other protein GTPases acting in the ribosomal cycle
  • 8.4.2.1 EF-G
  • 8.4.3 Further ribosome studies
  • 8.4.4 Eukaryotic ribosomes
  • References
  • tRNA-synthetases
  • bksec2_5
  • Reverse Transcriptases (RT)
  • bksec2_6
  • snRPs
  • bksec2_7
  • The Ribosome
  • bksec2_8
  • Further reading
  • Books
  • Index
  • Back Cover.

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