CHAPTER 2
DNA and RNA Structure
CONTENTS
2.1 Structures of Components 14
2.1.1 Nucleosides and Nucleotides 14
2.1.2 Physical Properties of Nucleosides and Nucleotides 16
2.1.3 Spectroscopic Properties of Nucleosides and Nucleotides 19
2.1.4 Shapes of Nucleotides 20
2.2 Standard DNA Structures 24
2.2.1 Primary Structure of DNA 24
2.2.2 Secondary Structure of DNA 24
2.2.3 A-DNA 27
2.2.4 The B-DNA Family 30
2.2.5 Z-DNA 31
2.3 Real DNA Structures 33
2.3.1 Sequence-Dependent Modulation of DNA Structure 33
2.3.2 Mismatched Base–Pairs 36
2.3.3 Unusual DNA Structures 38
2.3.4 B–Z Junctions and B–Z Transitions 45
2.3.5 Circular DNA and Supercoiling 46
2.3. 6Triple-Stranded DNA 49
2.3.7 Other Non-Canonical DNA Structures 52
2.4 Structures of RNA Species 55
2.4.1 Primary Structure of RNA 56
2.4.2 Secondary Structure of RNA: A-RNA and A-RNA 57
2.4.3 RNADNA Duplexes 59
2.4.4 RNA Bulges, Hairpins and Loops 61
2.4.5 Triple-Stranded RNAs 64
2.5 Dynamics of Nucleic Acid Structures 64
2.5.1 Helix-Coil Transitions of Duplexes 64
2.5.2 DNA Breathing 66
2.5.3 Energetics of the B–Z Transition 67
2.5.4 Rapid DNA Motions 68- 6Higher-Order DNA Structures 68
2.6.1 Nucleosome Structure 68
2.6.2 Chromatin Structure 69
References 72