Nucleic Acids Biochemistry

  1. Structure of Deoxyribonucleic Acid (DNA)
    1. Primary Structure
      1. Polynucleotide Chain Formation
        1. Phosphodiester Bond Formation
          1. Chain Directionality
            1. Backbone Composition
            2. Phosphodiester Backbone
              1. Sugar-Phosphate Linkages
                1. Backbone Flexibility
                  1. Electrostatic Properties
                  2. 5' and 3' Ends
                    1. Terminal Phosphate Groups
                      1. Hydroxyl Group Orientation
                        1. Polarity Significance
                        2. Directionality of DNA Strands
                          1. 5' to 3' Direction
                            1. Antiparallel Arrangement
                              1. Functional Implications
                              2. Base Sequence and Notation
                                1. Sequence Representation
                                  1. Reading Conventions
                                    1. Complementary Sequences
                                  2. Secondary Structure: The Double Helix
                                    1. Watson-Crick Base Pairing
                                      1. Hydrogen Bonding Patterns
                                        1. A-T Base Pair Geometry
                                          1. G-C Base Pair Geometry
                                            1. Bond Lengths and Angles
                                            2. Complementarity Rules
                                              1. Purine-Pyrimidine Pairing
                                                1. Geometric Constraints
                                                  1. Thermodynamic Stability
                                                  2. Base Pair Stability
                                                    1. Hydrogen Bond Strength
                                                      1. Stacking Interactions
                                                        1. Solvent Effects
                                                      2. Antiparallel Orientation of Strands
                                                        1. Strand Polarity
                                                          1. Structural Consequences
                                                            1. Functional Significance
                                                            2. Groove Structure
                                                              1. Major Groove Dimensions
                                                                1. Minor Groove Dimensions
                                                                  1. Protein Recognition Sites
                                                                    1. Accessibility Patterns
                                                                    2. Helical Parameters
                                                                      1. Pitch Measurements
                                                                        1. Diameter Specifications
                                                                          1. Base Pairs per Turn
                                                                            1. Rise per Base Pair
                                                                            2. Physical Properties of the Double Helix
                                                                              1. Denaturation Process
                                                                                1. Thermal Denaturation
                                                                                  1. Chemical Denaturation
                                                                                    1. pH Effects
                                                                                    2. Renaturation Process
                                                                                      1. Annealing Conditions
                                                                                        1. Kinetics of Renaturation
                                                                                          1. Specificity Requirements
                                                                                          2. Melting Temperature
                                                                                            1. Definition and Measurement
                                                                                              1. Cooperative Melting
                                                                                                1. Hyperchromic Effect
                                                                                                2. Factors Affecting Melting Temperature
                                                                                                  1. GC Content Effects
                                                                                                    1. Ionic Strength Influence
                                                                                                      1. pH Effects
                                                                                                        1. Solvent Composition
                                                                                                    2. Alternative DNA Conformations
                                                                                                      1. B-DNA Structure
                                                                                                        1. Structural Features
                                                                                                          1. Right-Handed Helix
                                                                                                            1. Base Pair Geometry
                                                                                                              1. Groove Dimensions
                                                                                                              2. Biological Relevance
                                                                                                                1. Physiological Conditions
                                                                                                                  1. Protein Interactions
                                                                                                                    1. Functional Significance
                                                                                                                  2. A-DNA Structure
                                                                                                                    1. Structural Features
                                                                                                                      1. Right-Handed Helix
                                                                                                                        1. Compressed Structure
                                                                                                                          1. Altered Groove Dimensions
                                                                                                                          2. Conditions Favoring A-DNA
                                                                                                                            1. Low Humidity
                                                                                                                              1. Ethanol Presence
                                                                                                                                1. Dehydration Effects
                                                                                                                              2. Z-DNA Structure
                                                                                                                                1. Structural Features
                                                                                                                                  1. Left-Handed Helix
                                                                                                                                    1. Zigzag Backbone
                                                                                                                                      1. Altered Base Pairing
                                                                                                                                      2. Biological Significance
                                                                                                                                        1. Regulatory Sequences
                                                                                                                                          1. Transcriptional Control
                                                                                                                                            1. Chromatin Structure
                                                                                                                                          2. Other DNA Forms
                                                                                                                                            1. Bent DNA
                                                                                                                                              1. Cruciform Structures
                                                                                                                                                1. Triple Helix DNA
                                                                                                                                              2. Higher-Order DNA Structure
                                                                                                                                                1. DNA Supercoiling
                                                                                                                                                  1. Types of Supercoiling
                                                                                                                                                    1. Positive Supercoiling
                                                                                                                                                      1. Negative Supercoiling
                                                                                                                                                        1. Relaxed DNA
                                                                                                                                                        2. Biological Importance
                                                                                                                                                          1. Transcriptional Regulation
                                                                                                                                                            1. Replication Control
                                                                                                                                                              1. Chromatin Compaction
                                                                                                                                                              2. Topoisomerases
                                                                                                                                                                1. Type I Topoisomerases
                                                                                                                                                                  1. Mechanism of Action
                                                                                                                                                                    1. Single-Strand Break Formation
                                                                                                                                                                      1. Relaxation of Supercoils
                                                                                                                                                                      2. Type II Topoisomerases
                                                                                                                                                                        1. Mechanism of Action
                                                                                                                                                                          1. Double-Strand Break Formation
                                                                                                                                                                            1. ATP Requirement
                                                                                                                                                                        2. Chromatin Structure in Eukaryotes
                                                                                                                                                                          1. Histone Proteins
                                                                                                                                                                            1. Core Histones
                                                                                                                                                                              1. H2A Structure and Function
                                                                                                                                                                                1. H2B Structure and Function
                                                                                                                                                                                  1. H3 Structure and Function
                                                                                                                                                                                    1. H4 Structure and Function
                                                                                                                                                                                    2. Linker Histone
                                                                                                                                                                                      1. H1 Structure and Function
                                                                                                                                                                                        1. Chromatin Compaction Role
                                                                                                                                                                                      2. Nucleosome Structure
                                                                                                                                                                                        1. Core Particle Organization
                                                                                                                                                                                          1. DNA Wrapping Pattern
                                                                                                                                                                                            1. Histone Octamer Assembly
                                                                                                                                                                                              1. Linker DNA Regions
                                                                                                                                                                                              2. Chromatin Fiber Organization
                                                                                                                                                                                                1. 30-nm Fiber Structure
                                                                                                                                                                                                  1. Higher-Order Folding
                                                                                                                                                                                                    1. Scaffold Proteins
                                                                                                                                                                                                    2. Chromatin Loops and Domains
                                                                                                                                                                                                      1. Loop Organization
                                                                                                                                                                                                        1. Topological Domains
                                                                                                                                                                                                          1. Boundary Elements
                                                                                                                                                                                                          2. Euchromatin Properties
                                                                                                                                                                                                            1. Open Chromatin Structure
                                                                                                                                                                                                              1. Transcriptional Activity
                                                                                                                                                                                                                1. Histone Modifications
                                                                                                                                                                                                                2. Heterochromatin Properties
                                                                                                                                                                                                                  1. Condensed Chromatin Structure
                                                                                                                                                                                                                    1. Transcriptional Silencing
                                                                                                                                                                                                                      1. Repetitive DNA Content
                                                                                                                                                                                                                      2. Higher-Order Chromosome Structure
                                                                                                                                                                                                                        1. Metaphase Chromosome Organization
                                                                                                                                                                                                                          1. Condensin Proteins
                                                                                                                                                                                                                            1. Chromosome Territories

                                                                                                                                                                                                                      Previous

                                                                                                                                                                                                                      2. Chemical Composition of Nucleic Acids

                                                                                                                                                                                                                      Go to top

                                                                                                                                                                                                                      Next

                                                                                                                                                                                                                      4. Structure and Diversity of Ribonucleic Acid (RNA)