Topology and Physics of Circular DNA presents comprehensive coverage of the physical properties of circular DNA. The author examines how topological constraints arising from cyclization of DNA lead to distinctive properties that make closed molecules radically different from linear DNA. The phenomenon of supercoiling, its geometric and topological analysis, and the formation of noncanonical structures in circular DNA under the influence of supercoiling are emphasized. The combination of consistent theoretical analysis and detailed treatment of major experimental approaches make Topology and Physics of Circular DNA an important reference volume for biophysicists, biochemists, molecular biologists, and researchers and students who want to expand their understanding of circular DNA.
Table of Contents
Foreword. Introduction. BASIC PHYSICAL PROPERTIES OF DNA. DNA STRUCTURE. Single-Stranded DNA. The Double Helix. Alternative Forms of the Double Helix. Other Regular Structures. Hairpins and Cruciform Structures. FLEXIBILITY OF THE DOUBLE HELIX. Macromolecular Conformation in Solution. Chains with Correlated Direction of Adjacent Links. Persistence Length of DNA. Excluded Volume Effect. Torsional Rigidity of the Double Helix. CONFORMATIONAL TRANSITIONS. General Properties of Conformational Transitions. Statistical-Mechanical Treatment of Conformational Transitions. Helix-Coil Transition. B-A Transition. B-Z Transition. CIRCULAR DNA AND SUPERCOILING. THE CIRCULAR FORM OF DNA. The Discovery of Circular DNA. The Topological Aspect of Inter-Strand Linkage. Linking Number Difference and Superhelical Density: Topoisomers. EXPERIMENTAL STUDIES OF SUPERCOILING. Determining the Linking Number Difference. The Dependence of Superhelical Density on Solution Conditions. Superhelicity of Circular DNA Isolated from Cells. Obtaining DNA with a Preset Superhelical Density. SUPERCOILING ENERGY. TOPOISOMERASES. GEOMETRY AND TOPOLOGY OF CIRCULAR DNA. RIBBON THEORY. Writhe and Twist. Principal Properties of Writhe. CONFORMATIONS OF SUPERCOILED DNA. Torsional Rigidity of the Double Helix. Computer Simulation of Supercoiling. Experimental Studies of Supercoiled DNA Conformations. Thermodynamics of Supercoiling. CYCLIZATION OF DNA. KNOTTED AND LINKED DNA. Types of Knots and Linkages. Theoretical Analysis of Knots and Linkages. Knots and Linkages in DNA. Topological Approach to the Study of the Mechanisms of Enzymatic Reactions. FORMATION OF NONCANONICAL STRUCTURES UNDER THE IMPACT OF NEGATIVE SUPERCOILING. EXPERIMENTAL METHODS OF ANALYSIS OF NONCANONICAL STRUCTURES IN CIRCULAR DNA. Methods of Localization of Structural Transitions. The Method of Two-Dimensional Gel Electrophoresis. THERMODYNAMIC ANALYSIS OF THE FORMATION OF NONCANONICAL STRUCTURES. CRUCIFORM STRUCTURES. THE LEFT-HANDED Z-FORM. MELTING OF CLOSED CIRCULAR DNA. THE H-FORM. THE INFLUENCE OF SUPERCOILING ON THE B-A TRANSITION. STATISTICAL-MECHANICAL ANALYSIS. MUTUAL INFLUENCE AND COMPETITION OF DIFFERENT STRUCTURAL TRANSITIONS. KINETICS OF THE FORMATION OF NONCANONICAL STRUCTURES IN CIRCULAR DNA. THE USE OF CIRCULAR DNA IN STUDIES OF THE DOUBLE HELIX AND ITS GENERAL PROPERTIES. FINDING THE HELICAL REPEAT OF THE DOUBLE HELIX. FINDING THE DOUBLE HELIX UNWINDING ANGLE UPON LIGAND BINDING. DNA SUPERCOILING INSIDE THE CELL. SUPERHELICAL STRESS. EXISTENCE OF NONCANONICAL STRUCTURE WITHIN A CELL. TRANSCRIPTION-INDUCED DNA SUPERCOILING.
Alexander V. Vologodskii is Research Professor of Chemistry Department of Chemistry New York University.