Elsevier S & T

Principles of Nucleic Acid Structure

Neidle, Stephen

In stock
No reviews
32.250 KD inc. VAT
License
Table of contents
  • Dedication Pagev
  • Prefacevii
  • Contentsix
  • Chapter 1: Methods for Studying Nucleic Acid Structure1
  • 1.1 Introduction1
  • 1.2 X-ray Diffraction Methods for Structural Analysis2
  • 1.2.1 Overview2
  • 1.2.2 Fiber Diffraction Methods5
  • 1.2.3 Single-Crystal Methods7
  • 1.3 NMR Methods for Studying Nucleic Acid Structure and Dynamics10
  • 1.4 Molecular Modelling and Simulation of Nucleic Acids11
  • 1.5 Chemical, Enzymatic, and Biophysical Probes of Structure and Dynamics14
  • 1.6 Sources of Structural Data15
  • 1.7 Visualization of Nucleic Acid Molecular Structures15
  • 1.7.1 The Structures in This Book16
  • References16
  • Further Reading17
  • Chapter 2: The Building-Blocks of DNA and RNA20
  • 2.1 Introduction20
  • 2.2 Base Pairing23
  • 2.3 Base and Base Pair Flexibility24
  • 2.4 Sugar Puckers28
  • 2.5 Conformations About the Glycosidic Bond32
  • 2.6 The Backbone Torsion Angles and Correlated Flexibility33
  • References36
  • Further Reading37
  • Chapter 3: DNA Structure as Observed in Fibers and Crystals38
  • 3.1 Structural Fundamentals38
  • 3.1.1 Helical Parameters38
  • 3.1.2 Base-Pair Morphological Features38
  • 3.2 Polynucleotide Structures from Fiber Diffraction Studies39
  • 3.2.1 Classic DNA Structures39
  • 3.2.2 DNA Polymorphism in Fibers43
  • 3.3 B-DNA Oligonucleotide Structure as Seen in Crystallographic Analyses47
  • 3.3.1 The Dickerson–Drew Dodecamer47
  • 3.3.2 Other Studies of the Dickerson–Drew Dodecamer49
  • 3.3.3 Other B-DNA Oligonucleotide Structures51
  • 3.3.4 Sequence-Dependent Features of B-DNA: Their Occurrence and Their Prediction56
  • 3.4 A-DNA Oligonucleotide Crystal Structures60
  • 3.4.1 A-Form Octanucleotides60
  • 3.4.2 Do A-Form Oligonucleotides Occur in Solution? Crystal-Packing Effects61
  • 3.4.3 The A harr B Transition in Crystals63
  • 3.5 Z-DNA – Left-Handed DNA64
  • 3.5.1 The Z-DNA Hexanucleotide Crystal Structure64
  • 3.5.2 Overall Structural Features65
  • 3.5.3 The Z-DNA Helix66
  • 3.5.4 Other Z-DNA Structures67
  • 3.5.5 Biological Aspects of Z-DNA67
  • 3.6 Bent DNA69
  • 3.6.1 DNA Periodicity in Solution69
  • 3.6.2 A-Tracts and Bending70
  • 3.6.3 Structures Showing Bending71
  • 3.6.4 The Structure of Poly dAmiddotdT73
  • 3.7 Concluding Remarks74
  • References74
  • Further Reading80
  • Chapter 4: Nonstandard and Higher-Order DNA Structures: DNA–DNA Recognition81
  • 4.1 Mismatches in DNA81
  • 4.1.1 General Features81
  • 4.1.2 Purine:Purine Mismatches82
  • 4.1.3 Alkylation Mismatches85
  • 4.2 DNA Triple Helices88
  • 4.2.1 Introduction88
  • 4.2.2 Structural Studies90
  • 4.2.3 Antiparallel Triplexes and Nonstandard Base-pairings95
  • 4.2.4 Triplex Applications100
  • 4.3 Guanine Quadruplexes101
  • 4.3.1 Introduction101
  • 4.3.2 Overall Structural Features of Quadruplex DNA103
  • 4.3.3 Examples of Simple Quadruplex Structures107
  • 4.3.4 Some Complex Quadruplex Structures108
  • 4.3.5 The i-Motif113
  • 4.4 DNA Junctions114
  • 4.4.1 Holliday Junction Structures114
  • 4.4.2 DNA Enzyme Structures118
  • 4.5 Unnatural DNA Structures120
  • References124
  • Further Reading131
  • Chapter 5: Principles of Small Molecule-DNA Recognition132
  • 5.1 Introduction132
  • 5.2 DNA-Water Interactions136
  • 5.2.1 Hydration in the Grooves in Detail140
  • 5.3 General Features of DNA-Drug and Small-Molecule Recognition143
  • 5.4 Intercalative Binding144
  • 5.4.1 Simple Intercalators146
  • 5.4.2 Complex Intercalators147
  • 5.4.3 Major-Groove Intercalation151
  • 5.4.4 Bis-Intercalators158
  • 5.5 Intercalative-Type Binding to Higher-Order DNAs163
  • 5.5.1 Triplex DNA–Ligand Interactions163
  • 5.5.2 Ligand Binding to Quadruplex DNAs164
  • 5.5.3 Ligand Binding to Junction DNAs166
  • 5.6 Groove-Binding Molecules169
  • 5.6.1 Simple Groove Binding Molecules169
  • 5.6.2 Netropsin and Distamycin178
  • 5.6.3 Sequence-Specific Polyamides182
  • 5.7 Small Molecule Covalent Bonding to DNA187
  • 5.7.1 The Platinum Drugs188
  • 5.7.2 Covalent-Binding Combined with Sequence-Specific Recognition191
  • References195
  • Further Reading202
  • Chapter 6: RNA Structures and Their Diversity204
  • 6.1 Introduction204
  • 6.2 Fundamentals of RNA Structure206
  • 6.2.1 Helical RNA Conformations206
  • 6.2.2 Mismatched and Bulged RNA Structures210
  • 6.3 Transfer RNA Structures217
  • 6.4 Ribozymes221
  • 6.4.1 The Hammerhead Ribozyme223
  • 6.4.2 Complex Ribozymes224
  • 6.5 Riboswitches227
  • 6.6 The Ribosome, a Ribozyme Machine229
  • 6.6.1 The Structure of the 30S Subunit232
  • 6.6.2 The Structure of the 50S subunit234
  • 6.6.3 Complete Ribosome Structures234
  • 6.7 RNA-Drug Complexes235
  • 6.8 RNA Motifs241
  • 6.9 Web Sites of Interest243
  • References244
  • Further Reading248
  • Chapter 7: Principles of Protein-DNA Recognition249
  • 7.1 Introduction249
  • 7.2 Direct Protein-DNA Contacts252
  • 7.3 Major-Groove Interactions – the alpha-Helix as the Recognition Element257
  • 7.4 Zinc-Finger Recognition Modes259
  • 7.5 Other Major Groove Recognition Motifs263
  • 7.6 Minor-Groove Recognition264
  • 7.6.1 Recognition of B-DNA264
  • 7.6.2 The Opening-up of the Minor Groove by TBP267
  • 7.6.3 Other Proteins that Induce Bending of DNA268
  • 7.7 DNA-Bending and Protein Recognition272
  • 7.8 Protein-DNA-Small Molecule Recognition275
  • Useful Websites278
  • References278
  • Further Reading282
  • Index283
Book details
  • Vendor Elsevier S & T
  • SKU 9780123695079
  • ISBN-13 9780080553528
  • Author Neidle, Stephen
  • Edition 2nd
  • Category Science
  • Subject Biochemistry

Do you have questions about this book?

Ask an expert!

Description eBook delivery & access Reviews
This unique and practical resource provides the most complete and concise summary of underlying principles and approaches to studying nucleic acid structure, including discussion of x-ray crystallography, NMR, molecular modelling, and databases. Its focus is on a survey of structures especially important for biomedical research and pharmacological applications. To aid novices, the book includes an introduction to technical lingo used to describe nucleic acid structure and conformations (roll, slide, twist, buckle, etc.). This completely updated edition features expanded coverage of the latest advances relevant to recognition of DNA and RNA by small molecules and proteins. In particular, the reader will find extensive new discussions on: RNA folding, ribosome structure and antibiotic interactions, DNA quadruplexes, DNA and RNA protein complexes, and short interfering RNA (siRNA). This handy guide ends with a complete list of resources, including relevant online databases and software.

* Completely updated with expanded discussion of topics such as RNA folding, ribosome structure and antibiotic interactions, DNA quadruplexes, DNA and RNA protein complexes, and short interfering RNA (siRNA)
* Includes a complete list of resources, including relevant online databases and software
* Defines technical lingo for novices