Nucleic acids : structures, properties, and functions

Başlık:

Yazar:

Bloomfield, Victor A.

ISBN:

9780935702491

Ek Yazar:

Bloomfield, Victor A.

Yayım Bilgisi:

Sausalito, Calif. : University Science Books, c2000.

Fiziksel Tanım:

x, 794 p. : ill. ; 26 cm.

Contents:

Introduction -- Bases, nucleosides, and nucleotides -- Chemical and enzymatic methods -- Nucleic acid structures from diffraction methods -- Structure and dynamics by NMR -- Electronic and vibrational spectroscopy -- Theoretical methods -- Conformational changes -- Size and shape of nucleic acids in solution -- Supercoiled DNA -- Interaction of nucleic acids and water and ions -- Interaction and reaction with drugs -- Protein-nucleic acid interactions -- Higher order structure.

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Library	Materyal Türü	Barkod	Yer Numarası	Durum
Searching... Pamukkale Merkez Kütüphanesi	Kitap	0034215	QP620.B64 2000	Searching... Unknown

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Özet

Nucleic Acids presents an up-to-date and comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function. With a targeted audience of 1) molecular biologists, 2) physical biochemists, and 3) physical chemists, the book has been carefully organized to reach three different audiences while requiring only introductory physical chemistry and molecular biology as prerequisites. Nucleic Acids will serve as a textbook in physical biochemistry and biophysical chemistry classes, as well as a supplemental text in courses on nucleic acid biochemistry or molecular biology, and as a personal reference for students and researchers in these fields. Key Features Organized according to a systematic consideration of techniques used in the study of nucleic acid structure and properties. Key topics - such as protein-DNA and protein-drug complexes, conformational transitions, characterization of nucleic acids by gel and solution techniques, and behavior of supercoiled DNA - are covered in great detail as veritable mini-monographs. Heavily illustrated with diagrams, graphs, and molecular structures, including nearly 2 dozen color figures. Includes numerous figures, tables and an extensive bibliography to facilitate use as a reference volume.

Preface	p. ix
Chapter 1 Introduction	p. 1
1. Biological Roles of the Nucleic Acids	p. 1
2. Physical Chemistry and Nucleic Acid Function	p. 2
3. Outline of this Book	p. 3
4. Obtaining Nucleic Acids for Physical Chemical Study	p. 6
5. The Periodical Literature of Nucleic Acids	p. 7
6. Books and Monographs	p. 8
7. Computer Analysis of Sequences and Structures	p. 10
References	p. 10
Chapter 2 Bases, Nucleosides, and Nucleotides	p. 13
1. Structures	p. 13
2. Electron Distributions	p. 22
3. Base Pairing and Base Stacking	p. 31
References	p. 41
Chapter 3 Chemical and Enzymatic Methods	p. 45
1. Introduction	p. 45
2. Synthesis and Hydrolysis	p. 46
3. Determination of Sequence	p. 52
4. Determination of Secondary Structure	p. 58
5. Determination of Tertiary Structure	p. 69
References	p. 72
Chapter 4 Nucleic Acid Structures from Diffraction Methods	p. 79
1. Introduction	p. 79
2. Diffraction Methods	p. 80
3. General Features of Duplex DNA and RNA Structure	p. 87
4. Detailed Structure and Sequence Dependence of Double-Stranded DNA	p. 93
5. Double-Helical RNA Duplex	p. 100
6. DNA Helices with Imperfect Base Pairing	p. 101
7. Local Mobility of Double Helical Nucleic Acids	p. 102
8. Transfer RNA	p. 103
References	p. 108
Chapter 5 Structure and Dynamics by NMR	p. 111
1. Introduction to NMR Methods	p. 112
2. Systematic Assignment of Resonances	p. 122
3. Parameters for Structure Analysis	p. 134
4. Characterization of Structures	p. 141
5. Dynamic Analysis	p. 146
6. Examples of NMR Studies of Nucleic Acids	p. 150
7. Conclusions	p. 158
References	p. 158
Chapter 6 Electronic and Vibrational Spectroscopy	p. 165
1. Electronic Absorption Spectra in the Ultraviolet	p. 166
2. Fluorescence and Phosphorescence	p. 181
3. Circular Dichroism	p. 185
4 Linear Dichroism	p. 199
5. Infrared Absorption and Raman Scattering	p. 207
References	p. 217
Chapter 7 Theoretical Methods	p. 223
1. Theoretical Foundations	p. 223
2. Simulation Methods	p. 230
3. Theoretical Rationale for Conformational Preferences of Nucleic Acid Components	p. 239
4. Sequence-Dependent Effects within Helices	p. 242
5. Mismatches, Damaged DNA, and DNA-Drug Interactions	p. 249
6. Concluding Perspectives	p. 253
References	p. 254
Chapter 8 Conformational Changes	p. 259
1. Single-Strand Stacking	p. 261
2. Double Helix Formation by Oligonucleotides without Loops	p. 271
3. Double Helix Formation by Oligonucleotides with Loops	p. 291
4. Double Helix Formation with Polynucleotides	p. 302
5. Environmental Effects on Helix Stability	p. 307
6. Triple Helixes	p. 310
7. G-Quartets	p. 311
8. Predicting Secondary Structure	p. 312
9. Predicting Three-Dimensional Structure	p. 315
10. Helix-Helix Transitions	p. 317
Appendix	p. 317
References	p. 321
Chapter 9 Size and Shape of Nucleic Acids in Solution	p. 335
1. Characterization at the Macromolecular Level	p. 336
2. Models for Molecular Structure	p. 337
3. Frictional Coefficients for Model Shapes	p. 341
4. Electrophoresis	p. 345
5. Sedimentation Velocity	p. 354
6. Diffusion	p. 360
7. Sedimentation Equilibrium	p. 364
8. Viscosity	p. 368
9. Viscoelasticity	p. 369
10. Rotational Dynamics	p. 372
11. Scattering	p. 381
12. Dynamic Light Scattering	p. 390
13. Microscopy: Visualization of Single Molecules	p. 396
14. Bending and Twisting of DNA	p. 407
References	p. 433
Chapter 10 Supercoiled DNA	p. 443
1. Introduction	p. 443
2. Topoisomerases and Gyrases	p. 444
3. Geometry and Topology of DNA Supercoiling	p. 446
4. Energetics of Twisting and Bending	p. 463
5. Stress-Induced Reactions	p. 466
References	p. 470
Chapter 11 Interaction of Nucleic Acids and Water and Ions	p. 475
1. Hydration	p. 476
2. Polyelectrolyte Behavior	p. 488
3. Hydration in Ionic Solutions	p. 504
4. Specific Binding of Metal Ions and Polyamines	p. 507
5. Mixed Aqueous-Nonaqueous Solvents	p. 521
Appendix	p. 522
References	p. 528
Chapter 12 Interaction and Reaction with Drugs	p. 535
1. Modes of Interaction: Intercalation and Groove Binding	p. 536
2. Theoretical Description of Binding Equilibria	p. 537
3. Experimental Studies of Binding Equilibria	p. 547
4. Solution Studies of the Structure of Drug-DNA Complexes	p. 565
5. Kinetics of Ligand Binding	p. 571
6. Natural Products that React Covalently with DNA	p. 575
7. Synthetic DNA Binding Agents	p. 585
References	p. 591
Chapter 13 Protein-Nucleic Acid Interactions	p. 597
1. Biological Role of Protein-Nucleic Acid Interactions	p. 598
2. Elementary Energetics and Specificity of Interaction	p. 601
3. DNA Sequence Motifs	p. 615
4. Twisting and Bending of DNA Sequences in Protein Complexes	p. 626
5. Looping of DNA Sequences	p. 641
6. Structural Motifs in Sequence Specific DNA-Protein Interactions	p. 645
7. Motifs in RNA-Protein Interactions	p. 677
8. Structural Motifs in Enzymes that Act on Nucleic Acids	p. 683
9. Solution Characterization of Binding Interactions	p. 692
10. Kinetics and the Search Mechanism	p. 704
References	p. 711
Chapter 14 Higher Order Structure	p. 725
1. DNA Condensation in Vitro	p. 725
2. DNA Packaging in Bacteriophage and Bacteria	p. 749
3. DNA Packaging in Eukaryotes	p. 756
References	p. 766
Index	p. 775

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