Modified nucleosides: in biochemistry, biotechnology, and medicine/ edited by Piet Herdewijn.

Includes bibliographical references and index.

Modified Nucleosides; Contents; Preface; List of Contributors; Part I Biochemistry and Biophysics; 1 Investigations on Fluorine-Labeled Ribonucleic Acids by (19)F NMR Spectroscopy; 1.1 Introduction; 1.1.1 NMR Spectroscopic Properties of the (19)F Nucleus; 1.1.1.1 General NMR Spectroscopic Properties; 1.1.1.2 (19)F versus (1)H NMR Spectroscopy; 1.1.1.3 Factors Affecting the (19)F Chemical Shift in Biomolecules; 1.1.1.4 Fluorine Relaxation in Biological Systems; 1.1.1.5 Solvent-Induced Isotope Shifts of (19)F NMR Resonances; 1.1.2 (19)F NMR Spectroscopy of Proteins 1.1.2.1 Incorporation of Fluorinated Amino Acids into Proteins1.1.2.2 (19)F NMR Spectroscopic Studies of Proteins; 1.2 (19)F NMR Spectroscopy of Nucleic Acids; 1.2.1 Nucleic Acids with Fluorinated Nucleobases; 1.2.1.1 Transfer RNAs; 1.2.1.2 HhaI Methyltransferase in Complex with DNA Duplexes; 1.2.1.3 Minimal Hammerhead Ribozyme; 1.2.1.4 HIV TAR RNA; 1.2.2 Nucleic Acids with Fluorinated Ribose Units; 1.2.2.1 R1inv RNA; 1.2.2.2 RNA Secondary Structure Equilibria; 1.2.2.3 RNA Ligand Binding; 1.2.3 Influence of Fluorine Modifications on Nucleic Acid Structure; 1.3 Conclusions; References 2 8-Oxo-7,8-Dihydro-2 ́-Deoxyguanosine: A Major DNA Oxidation Product2.1 Introduction; 2.2 Formation of 8-Oxo-7,8-Dihydroguanine; 2.2.1 Single Lesion; 2.2.1.1 ·OH Radical; 2.2.1.2 One-Electron Oxidation; 2.2.1.3 Singlet Oxygen; 2.2.2 Tandem Lesions; 2.3 Reactivity of 8-Oxo-7,8-Dihydro-2 ́-Deoxyguanosine; 2.3.1 One-Electron Oxidation; 2.3.1.1 Secondary Oxidation Products; 2.3.1.2 DNA-Protein Crosslinks; 2.3.2 Singlet Oxygen; 2.3.2.1 Nucleoside; 2.3.2.2 Oligonucleotide; 2.4 Formation of 8-Oxo-7,8-Dihydro-2 ́-Deoxyguanosine in Cellular DNA; 2.4.1 Methods of Measurement 2.4.1.1 HPLC Methods (HPLC-ECD and HPLC-MS/MS)2.4.1.2 Enzymic Assays; 2.4.2 Indirect Effects of Ionizing Radiation (·OH Radical); 2.4.3 High-Intensity UV Laser Irradiation (One-Electron Oxidation); 2.4.4 UVA Photosensitization ((1)O(2)); 2.5 Synthesis of 8-OxodGuo and Insertion into Oligonucleotides; 2.6 Conclusions; References; 3 Modified DNA Bases: Probing Base-Pair Recognition by Polymerases; 3.1 Introduction; 3.1.1 The Importance of Understanding DNA Polymerases; 3.1.2 The Utility of Modified Nucleobases in Probing Mechanisms; 3.1.3 The Scope of this Chapter 3.2 Basic Principles and Methods in Replication3.2.1 The Chemistry of Polymerases; 3.2.2 Different Classes of Polymerases; 3.2.3 Methods Used in Polymerase Studies; 3.3 Alternative Hydrogen-Bonding Schemes; 3.3.1 Thioguanine-Pyridone; 3.3.2 Benner Hydrogen-Bonding Variants; 3.4 Non-Polar Nucleoside Isosteres; 3.4.1 The Concept of Nucleobase Isosteres; 3.4.2 Synthesis, Structure, and Physical Properties; 3.4.3 Base-Pairing Properties; 3.4.4 Polymerase Behavior; 3.4.5 Other Classes of Polymerases; 3.4.6 Summary of Watson-Crick H-Bonding Effects in Polymerase Active Sites 3.5 Non-Polar Steric Probes