Category Books

Nucleic Acids: Structures, Properties, and Functions »

Authors: Donald M. Crothers, Victor A. Bloomfield, Ignacio Tinoco
ISBN-13: 9780935702491, ISBN-10: 0935702490
Format: Hardcover
Publisher: University Science Books
Date Published: March 2000
Edition: (Non-applicable)

Author Biography: Donald M. Crothers

Book Synopsis

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
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.

Booknews

Provides a detailed account of the structures and physical chemistry properties of nucleic acids, with an emphasis on the implications for biological function. The volume is organized to be of use to physical chemists, physical biochemists, and molecular biologists as well as students in those disciplines, requiring only a basic understanding of physical chemistry and molecular biology as prerequisites. Each chapter begins with a statement of the biological significance of each topic, followed by a presentation of the basic physical ideas and major results. Quantitative details are developed in special sections or appendices. Annotation c. Book News, Inc., Portland, OR (booknews.com)

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