Learn vital information about drug-DNA interactions from Drug-DNA Interactions: Structures and Spectra , the only comprehensive book written about this topic. Understand the types of structural and bonding information that can be obtained using specific physico-chemical methods and discover how to design new drugs that are more effective than current treatments and have fewer side effects. Find detailed information about X-ray crystallography, NMR spectroscopy, molecular modeling, and optical spectroscopy such as UV-Visible absorption, fluorescence, circular dichroism (CD), flow linear dichroism (FLD), infrared (IR) and Raman spectroscopy.
Author(s): Kazuo Nakamoto, Masamichi Tsuboi, Gary D. Strahan
Series: Methods of Biochemical Analysis
Edition: 1
Publisher: Wiley
Year: 2008
Language: English
Pages: 396
DRUG–DNA INTERACTIONS......Page 3
CONTENTS......Page 9
Preface......Page 13
Introduction......Page 15
1. DNA Structures and Spectra......Page 19
1.1.1. Primary (Chemical) Structure......Page 20
1.1.2. Bond Lengths and Bond Angles......Page 23
1.1.3. Canonical Structure of DNA: B-DNA......Page 27
1.1.4. Deoxyribose Moiety as a Flexible Joint......Page 31
1.1.5. Variations of B-DNA Structure......Page 33
1.1.6. Participation of Water Molecules in B-DNA Structure......Page 34
1.1.7. Partially Dehydrated Structure: A-DNA......Page 35
1.1.8. Internal Dihedral Angles......Page 37
1.1.9. Left-Handed Duplex: Z-DNA......Page 39
1.1.10. Superhelical Form of DNA......Page 41
1.1.11. Other Duplex Structures......Page 43
1.1.12. Higher-Order DNA Structures......Page 47
1.2.1. Ultraviolet Absorption Spectra......Page 52
1.2.2. Fluorescence Spectra......Page 55
1.2.3. Linear and Circular Dichroism......Page 56
1.3.1. Infrared Spectra of Bases......Page 60
1.3.2. Raman Spectra of Bases......Page 67
1.3.3. Vibrational Spectra of Nucleosides......Page 72
1.3.4. Vibrational Spectra of Nucleotides......Page 75
1.3.6. Vibrations of the Phosphodiester Linkage......Page 77
1.3.7. Infrared Spectra of DNA......Page 79
1.3.8. Raman Spectra of B-DNA......Page 81
1.3.9. Comparison of Raman Spectra of A- and B-DNA......Page 85
1.3.10. Raman Spectra of Z-DNA......Page 88
1.4. NMR Spectra......Page 90
1.4.1. NMR Signals and Magnetization Relaxation......Page 91
1.4.2. Proton NMR Spectra of Bases, Nucleosides, and Nucleotides......Page 94
1.4.3. Correlation Analysis, or "Spin–Spin Coupling"......Page 98
1.4.4. Nuclear Overhauser Effect......Page 103
1.4.5. Residual Dipolar Coupling......Page 112
1.5. Electron Spin Resonance Spectra......Page 113
1.6. X-Ray Crystallography......Page 114
1.6.1. Bragg Diffraction......Page 115
1.6.2. Diffraction of Helical DNA......Page 116
1.7.1. Molecular Modeling......Page 117
1.7.2. Modeling of Experimental Data......Page 118
References......Page 120
2. Intercalating Drugs......Page 137
2.1.1. X-Ray Diffraction Studies of Acridine–Dinucleoside Monophosphate Crystals......Page 140
2.1.2. Complexes with Longer DNAs: X-Ray and Modeling Analyses......Page 146
2.1.3. Unwinding Angle Measurements......Page 149
2.1.4. NMR Studies......Page 152
2.1.5. Fluorescence Spectra......Page 155
2.1.6. Flow Linear Dichroism Spectra/Studies......Page 158
2.1.7. Circular Dichroism Studies......Page 159
2.1.8. Biochemical Implications—a Few Examples......Page 160
2.2.1. X-Ray and Modeling Analyses of Ethidium Bromide–Dinucleoside Monophosphate Crystals......Page 161
2.2.2. Fiber X-Ray Diffraction Studies......Page 163
2.2.3. Visible Absorption Spectra......Page 166
2.2.4. Circular Dichroism Spectra......Page 168
2.2.5. Fluorescence Spectra......Page 170
2.2.6. Raman Spectra......Page 172
2.2.7. Electrophoresis Studies of DNA Unwinding......Page 177
2.2.8. Atomic Force Microscopy......Page 179
2.3.1. Absorption Spectroscopy......Page 183
2.3.2. (31)P NMR......Page 185
2.3.3. Exchangeable (1)H NMR Spectra......Page 186
2.3.4. Nonexchangeable (1)H NMR Spectra......Page 188
2.3.5. Raman Spectroscopy......Page 193
2.3.6. Unwinding......Page 194
2.4. Sequence Preference......Page 196
2.5. Bis- and Tris- Intercalators......Page 212
References......Page 217
3. Groove-Binding Drugs......Page 227
3.1. Netropsin and Distamycin......Page 228
3.2. Derivatives of Netropsin and Distamycin......Page 235
3.3. Hoechst 33258, SN6999, and Their Derivatives......Page 242
3.4. Chromomycin, Mithramycin, and Other GC Binders......Page 248
3.5. Groove Binding and Intercalation......Page 252
References......Page 258
4.1. (+)CC1065 and Related Drugs......Page 263
4.2. Anthramycin and Tomaymycin......Page 272
4.3. Ecteinascidins......Page 274
4.4. Mitomycins......Page 277
4.5. Intercalating Alkylators......Page 282
References......Page 289
5.1.1. Metal-Free Bleomycins......Page 293
5.1.2. Iron Complexes of Bleomycin......Page 297
5.1.3. Cobalt and Zinc Complexes of Bleomycin......Page 301
5.1.4. Model Compounds of Bleomycins......Page 306
5.2. Enediyne Antibiotics......Page 308
5.2.1. Calicheamicins......Page 309
5.2.2. Esperamicins......Page 312
5.2.3. Neocarzinostatin......Page 314
References......Page 317
6.1. Cisplatin......Page 321
6.1.1. Intrastrand Crosslinking Complexes......Page 322
6.2.1. Oxaliplatin and Carboplatin......Page 334
6.2.2. Platinum Complexes of Monofunctional Ligands......Page 336
6.2.3. Platinum Complexes of Chelating Ligands......Page 339
6.3. Transplatin and Derivatives......Page 345
6.4. Monofunctional Platinum Complexes......Page 350
6.5. Polynuclear and High-valent Platinum Complexes......Page 354
6.6. Complexes Containing Other Metals......Page 363
6.6.1. Palladium(II) and Gold(III)......Page 364
References......Page 365
A.1. Raman Tensor-Depolarization Ratio......Page 375
A.2.1. Origins of the Phenomenon......Page 377
A.2.2. Chemical Shift......Page 379
A.2.3. Magnetization Relaxation Processes......Page 380
A.3. Molecular Mechanics......Page 382
References......Page 384
Index......Page 385
