| Preface |
|
iii | |
| Contributors |
|
xvii | |
|
PART I. MECHANISMS OF DAMAGE RECOGNITION: THEORETICAL CONSIDERATIONS |
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1 | (64) |
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Dynamics of DNA Damage Recognition |
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3 | (18) |
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3 | (1) |
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Role of DNA Flexibility in Sequence-Dependent Activity of UDG |
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4 | (4) |
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Opening and Bending Dynamics of G•U Mismatches in DNA |
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8 | (5) |
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13 | (8) |
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15 | (6) |
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In Search of Damaged Bases |
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21 | (12) |
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21 | (1) |
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Mechanism for an Increased Rate of Target Site Location |
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21 | (2) |
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In Vitro Evidence for Processive Nicking Activity of DNA Glycosylases |
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23 | (3) |
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Discovery and Significance of In Vivo Processive Nicking Activity by T4-pdg |
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26 | (1) |
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DNA Bending as a Potential Prerequisite for Nucleotide Flipping |
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27 | (2) |
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Mechanisms of Nucleotide Flipping |
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29 | (1) |
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Specificity of Glycosylase Binding Sites and Catalytic Activities |
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30 | (3) |
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31 | (2) |
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Increased Specificity and Efficiency of Base Excision Repair Through Complex Formation |
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33 | (32) |
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33 | (3) |
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DNA Lesion Recognition and Removal |
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36 | (6) |
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42 | (4) |
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Gap Filling and Religation |
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46 | (3) |
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49 | (3) |
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52 | (2) |
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54 | (1) |
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54 | (11) |
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55 | (10) |
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PART II. UV DAMAGE AND OTHER BULKY DNA-ADDUCTS |
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65 | (232) |
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Structure and Properties of DNA Photoproducts |
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67 | (28) |
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67 | (2) |
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Cyclobutane Pyrimidine Dimers |
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69 | (10) |
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Other Dimer-Related Products |
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79 | (2) |
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81 | (5) |
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86 | (2) |
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88 | (1) |
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89 | (1) |
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90 | (5) |
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90 | (5) |
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Damage Recognition by DNA Photolyases |
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95 | (16) |
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95 | (1) |
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The Nature of the Substrates |
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96 | (1) |
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Characterization of Substrate Binding and Discrimination by Photolyases |
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97 | (1) |
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Interactions at the Photolyase-Photoproduct Interface: The Molecular Basis for Substrate Binding and Discrimination |
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98 | (7) |
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Substrate Binding In Vivo |
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105 | (2) |
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Summary and Future Directions |
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107 | (4) |
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107 | (4) |
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Damage Recognition by the Bacterial Nucleotide Excision Repair Machinery |
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111 | (28) |
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111 | (2) |
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Diversity of DNA Lesions Recognized |
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113 | (1) |
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The Proteins and Their Structural Domains |
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114 | (9) |
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Reaction Pathway for Damage Detection and Processing |
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123 | (7) |
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DNA Damage Recognition within the Biological Context of the Cell |
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130 | (3) |
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Similarities in Damage Recognition and Verification Between Bacterial and Eukaryotic Nucleotide Excision Repair Systems |
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133 | (6) |
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133 | (6) |
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Recognition of DNA Damage During Eukaryotic Nucleotide Excision Repair |
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139 | (26) |
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139 | (1) |
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Nucleotide Excision Repair Substrates |
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139 | (1) |
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140 | (2) |
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Subunits of the Eukaryotic NER Machinery |
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142 | (1) |
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Stepwise Assembly of the Mammalian NER Recognition Complex |
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143 | (1) |
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A Preassembled Repairosome in Yeast? |
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144 | (2) |
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Role of Damaged DNA Binding in Damage Recognition |
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146 | (1) |
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Recognition of Bulky Lesions During Transcription-Coupled DNA Repair |
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147 | (1) |
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Bipartite Substrate Discrimination in the GGR Pathway |
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148 | (1) |
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XPC-hHR23B as a Sensor of Defective Base Pairing |
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149 | (2) |
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Transcription Factor IIH as a Sensor of Defective Deoxyribonucleotide Chemistry |
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151 | (2) |
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Role of XPA-RPA in Integrating Different Recognition Signals |
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153 | (2) |
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Damage-Specific Recruitment of XPG and XPF-ERCC1 |
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155 | (1) |
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Regulation of the Damage Recognition Process |
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155 | (3) |
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158 | (7) |
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159 | (6) |
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Interactions of the Transcription Machinery with DNA Damage in Prokaryotes |
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165 | (16) |
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165 | (3) |
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The Behavior of RNA Polymerase Complexes with Different Types of DNA Damage |
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168 | (2) |
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The Behavior of RNA Polymerase Complexes at Lesions and NER |
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170 | (3) |
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The Behavior of RNA Polymerase Complexes at Lesions and BER |
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173 | (2) |
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Summary and Future Directions |
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175 | (6) |
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175 | (6) |
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DNA Repair in Actively Transcribed Genes in Eukaryotic Cells |
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181 | (20) |
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181 | (1) |
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Heterogeneity of DNA Repair |
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182 | (3) |
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Methods for Detecting TCR and GGR |
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185 | (3) |
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DNA Repair in Transcriptionally Active Genes in Different Organisms |
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188 | (5) |
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Models of TCR in Eukaryotic Cells |
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193 | (1) |
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Effect of Different Kinds of DNA Damage on TCR |
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194 | (7) |
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195 | (6) |
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Chromatin Structure and the Repair of UV Light-Induced DNA Damage |
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201 | (22) |
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201 | (1) |
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Nucleosomes: Heterogeneity in a Conserved Structure |
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202 | (1) |
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Dynamic Properties of Nucleosomes Regulate DNA Accessibility |
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203 | (5) |
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Damage Tolerance of Nucleosomes |
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208 | (1) |
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Repair of Nucleosomes by Photolyase |
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209 | (2) |
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Repair of Nucleosomes by NER |
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211 | (3) |
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Site-Specific Repair in Nucleosome and Damage Recognition |
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214 | (1) |
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Chromatin Remodeling and DNA Repair |
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214 | (2) |
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216 | (7) |
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216 | (7) |
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The Ultraviolet Damage Endonuclease (UVDE) Protein and Alternative Excision Repair: A Highly Diverse System for Damage Recognition and Processing |
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223 | (16) |
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223 | (1) |
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Discovery and Initial Characterization of S. pombe UVDE |
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224 | (2) |
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Recognition and Processing of UV Photoproducts |
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226 | (1) |
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Recognition and Processing of Platinum G-G Diadducts |
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227 | (1) |
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Recognition and Processing of Abasic Sites |
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227 | (2) |
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Modified Bases not Recognized by UVDE |
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229 | (1) |
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Recognition and Processing of Base-Base Mismatches |
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230 | (1) |
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Recognition and Processing of Insertion-Deletion Loops |
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231 | (1) |
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Subsequent Steps Following UVDE-Initiated Alternative Excision Repair |
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232 | (1) |
|
Schizosaccharomyces pombe UVDE Homologs |
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233 | (1) |
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234 | (5) |
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234 | (5) |
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Structural Aspects of Pt-DNA Adduct Recognition by Proteins |
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239 | (24) |
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239 | (1) |
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239 | (1) |
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Structural Consequences of Platinum-Binding to Double-Stranded DNA |
|
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240 | (5) |
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Recognition of cis-DDP-1,2 Intrastrand Cross-Link by Cellular Proteins |
|
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245 | (9) |
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254 | (9) |
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255 | (8) |
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Structural Aspects of Polycyclic Aromatic Carcinogen-Damaged DNA and Its Recognition by NER Proteins |
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263 | (34) |
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263 | (2) |
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Metabolism of PAH to Diol Epoxides and Formation of Stereoisomeric DNA Adducts |
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265 | (2) |
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267 | (2) |
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PAH-DNA Adducts: Conformational Motifs |
|
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269 | (4) |
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Insights into the Structural Motifs at the Nucleoside Adduct Level Derived from Computational Approaches |
|
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273 | (1) |
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PAH-DNA Adduct Conformational Motifs and NER |
|
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274 | (2) |
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Structural Differences Between Bay and Fjord Stereoisomeric PAH-N6-Adenine Adducts and Correlations with NER Susceptibilities |
|
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276 | (3) |
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279 | (10) |
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289 | (8) |
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290 | (7) |
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PART III. NON-BULKY BASE DAMAGE |
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297 | (164) |
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Structural Features of DNA Glycosylases and AP Endonucleases |
|
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299 | (24) |
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|
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The Base Excision Repair Pathway |
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299 | (1) |
|
DNA Glycosylase Structural Families |
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300 | (3) |
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Specific Mechanisms for Recognition of Damage |
|
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303 | (10) |
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313 | (2) |
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315 | (8) |
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315 | (8) |
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323 | (16) |
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Biological Consequences of Oxidative Damage |
|
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323 | (3) |
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Major Repair Enzymes that Recognize Oxidative Base Damage |
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326 | (7) |
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Repair Pathways for Oxidative DNA Damage |
|
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333 | (2) |
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|
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335 | (4) |
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335 | (4) |
|
Recognition of Alkylating Agent Damage in DNA |
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339 | (50) |
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|
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Modification of DNA by Small Alkylating Agents |
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339 | (2) |
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DNA Repair Systems for Removal of Alkylating Agent Damage |
|
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341 | (1) |
|
O6-Alkylguanine DNA Methyltransferases---AGTs |
|
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342 | (13) |
|
AlkB---2-oxoglutarate-Dependent Fe(II)-Dependent Oxygenases |
|
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355 | (7) |
|
DNA Glycosylases---Base Excision Repair |
|
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362 | (15) |
|
Nucleotide Excision Repair |
|
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377 | (12) |
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382 | (7) |
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389 | (14) |
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389 | (1) |
|
Lesions and Their Consequences |
|
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389 | (1) |
|
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390 | (3) |
|
Endonuclease V, An Enzyme Specific for Deaminated Purines |
|
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393 | (3) |
|
Hypoxanthine/Alkylpurine DNA Glycosylases |
|
|
396 | (3) |
|
Endonuclease VIII of E. coli |
|
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399 | (1) |
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399 | (4) |
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|
|
399 | (4) |
|
New Paradigms for DNA Base Excision Repair in Mammals |
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403 | (18) |
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403 | (1) |
|
Oxidized Base-Specific Glycosylases in E. coli and Mammals |
|
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404 | (12) |
|
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416 | (5) |
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|
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417 | (4) |
|
Recognition and Repair of Abasic Sites |
|
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421 | (24) |
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|
|
|
AP Site Formation and Biological Impact |
|
|
421 | (2) |
|
AP-DNA Dynamics and Structure |
|
|
423 | (2) |
|
|
|
425 | (1) |
|
AP Site Recognition and Processing |
|
|
426 | (6) |
|
AP Site Repair in General |
|
|
432 | (13) |
|
|
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436 | (9) |
|
Oxidative Mitochondrial DNA Damage Resistance and Repair |
|
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445 | (16) |
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|
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445 | (1) |
|
General Features of Human mtDNA |
|
|
446 | (3) |
|
Oxidative mtDNA Damage Resistance and Repair |
|
|
449 | (3) |
|
New Lessons About Oxidative mtDNA Damage from the Budding Yeast, S. cerevisiae, Genetic Model System |
|
|
452 | (3) |
|
Conclusions and New Horizons |
|
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455 | (6) |
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456 | (5) |
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461 | (32) |
|
Mechanism of DNA Mismatch Repair from Bacteria to Human |
|
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463 | (20) |
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463 | (3) |
|
Biochemistry of Mismatch Repair Proteins |
|
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466 | (3) |
|
Mechanism of Mismatch Repair |
|
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469 | (5) |
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|
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474 | (9) |
|
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475 | (8) |
|
Interaction of the Escherichia coli Vsr with DNA and Mismatch Repair Proteins |
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483 | (10) |
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483 | (2) |
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485 | (5) |
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Summary and Concluding Remarks |
|
|
490 | (3) |
|
|
|
490 | (3) |
|
PART V. REPLICATION AND BYPASS OF DNA LESIONS |
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493 | (86) |
|
Mechanism of Translesion DNA Synthesis in Escherichia coli |
|
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495 | (12) |
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495 | (1) |
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Translesion DNA Synthesis and the SOS Response |
|
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496 | (1) |
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497 | (1) |
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497 | (1) |
|
|
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498 | (1) |
|
Accessory Proteins Are Required for Lesion Bypass By Pol V |
|
|
499 | (2) |
|
Other DNA Polymerases Involved in TLS in E. coli |
|
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501 | (1) |
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502 | (5) |
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503 | (4) |
|
Mechanism of Bypass Polymerases in Eukaryotes |
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507 | (22) |
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507 | (2) |
|
Concepts of Translesion Synthesis |
|
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509 | (1) |
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510 | (3) |
|
Mechanistic Models of Translesion Synthesis |
|
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513 | (2) |
|
Translesion Synthesis of Various DNA Damage in Eukaryotes |
|
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515 | (5) |
|
Importance of Translesion Synthesis in Eukaryotic Biology |
|
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520 | (9) |
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521 | (8) |
|
Structural Features of Bypass Polymerases |
|
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529 | (20) |
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529 | (6) |
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DNA Synthesis by the DINB Family Members from the Sulfolobus Genus |
|
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535 | (6) |
|
DNA Binding and Lesion Bypass in Polη |
|
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541 | (2) |
|
Recruitment of Y-Family DNA Polymerases |
|
|
543 | (2) |
|
Lesion Specificity of the Y-Family DNA Polymerases |
|
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545 | (4) |
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546 | (3) |
|
Regulation of Damage Tolerance by the RAD6 Pathway |
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549 | (30) |
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549 | (1) |
|
Mechanisms of Damage Bypass |
|
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550 | (4) |
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554 | (12) |
|
Proliferating Cell Nuclear Antigen Modification by the Ubiquitin-Like Protein Sumo |
|
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566 | (1) |
|
Mechanistic Considerations |
|
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567 | (3) |
|
Interactions of the RAD6 Pathway with Other Factors |
|
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570 | (3) |
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573 | (6) |
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574 | (5) |
|
PART VI. DNA STRAND BREAKS |
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|
579 | (176) |
|
Biochemical and Cellular Aspects of Homologous Recombination |
|
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581 | (28) |
|
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581 | (1) |
|
DNA Double-Strand Break Repair Through Homologous Recombination |
|
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582 | (1) |
|
Biochemical Properties of Homologous Recombination Proteins |
|
|
582 | (4) |
|
Cellular Properties of Homologous Recombination Proteins |
|
|
586 | (23) |
|
|
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602 | (7) |
|
The Mechanism of Vertebrate Nonhomologous DNA End Joining and Its Role in Immune System Gene Rearrangements |
|
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609 | (20) |
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609 | (1) |
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Essential Aspects of Vertebrate Nonhomologous DNA End Joining (NHEJ) |
|
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609 | (4) |
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Overview of V(D)J Recombination and its Utilization of NHEJ in the Rejoining Process |
|
|
613 | (2) |
|
Overview of Immunoglobulin Class Switch Recombination and its Utilization of NHEJ in the Rejoining Process |
|
|
615 | (4) |
|
Points of Biochemical Detail in the NHEJ Pathway |
|
|
619 | (3) |
|
Special Aspects of NHEJ as it Relates to V(D)J Recombination |
|
|
622 | (1) |
|
Are There Multiple NHEJ Pathways? |
|
|
622 | (2) |
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|
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624 | (1) |
|
Future Avenues of Study of the NHEJ Pathway |
|
|
624 | (5) |
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|
624 | (5) |
|
Structural Aspects of Ku and the DNA-Dependent Protein Kinase Complex |
|
|
629 | (56) |
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629 | (5) |
|
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634 | (14) |
|
|
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648 | (7) |
|
DNA-PK, Telomeres and Genomic Stability |
|
|
655 | (7) |
|
|
|
662 | (23) |
|
|
|
663 | (22) |
|
Cellular Functions of Mammalian DNA Ligases |
|
|
685 | (20) |
|
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685 | (1) |
|
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686 | (1) |
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686 | (1) |
|
|
|
687 | (6) |
|
Cellular Functions of DNA Ligase |
|
|
693 | (12) |
|
|
|
697 | (8) |
|
The Mre11/Rad50/Nbs1 Complex |
|
|
705 | (18) |
|
|
|
|
|
705 | (1) |
|
|
|
706 | (4) |
|
Cellular Biochemistry of the Mre11 Complex |
|
|
710 | (4) |
|
Structural Biochemistry of the Mre11 Complex |
|
|
714 | (3) |
|
Unified Model, Conclusions, and Outlook |
|
|
717 | (6) |
|
|
|
718 | (5) |
|
Histone γ-H2AX Involvement in DNA Double-Strand Break Repair Pathways |
|
|
723 | (14) |
|
|
|
|
|
|
|
723 | (1) |
|
Formation and Detection of γ-Phosphorylation |
|
|
724 | (2) |
|
γ-Phosphorylation of H2A(X) Spans Megabase-Long Domains in Chromatin |
|
|
726 | (1) |
|
Kinases Involved in γ-Phosphorylation of H2A(X) Histone Family |
|
|
727 | (1) |
|
Recruitment of Repair Factors to γ-Phosphorylated Chromatin |
|
|
728 | (1) |
|
Models and Speculations About the Biological Role of γ-H2AX Foci |
|
|
729 | (8) |
|
|
|
732 | (5) |
|
DNA Strand-Break Recognition, Signaling, and Resolution: The Role of Poly(ADP-Ribose) Polymerases-1 and -2 |
|
|
737 | (18) |
|
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|
Josiane Menissier-de Murcia |
|
|
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737 | (1) |
|
|
|
737 | (2) |
|
Nick Sensor Function of PARP-1 |
|
|
739 | (4) |
|
Dual Role of DNA-Damage Induced PAR Synthesis: Break Signaling and Recruitment of XRCC1 |
|
|
743 | (4) |
|
No Cross-Talk Between PAR Synthesis and γ-H2AX Formation in Response to DNA-Strand Break Injury |
|
|
747 | (2) |
|
Conclusions and Future Prospects |
|
|
749 | (6) |
|
|
|
750 | (5) |
|
PART VII. PERCEPTION OF DNA DAMAGE FOR INITIATING REGULATORY RESPONSES |
|
|
755 | (86) |
|
Cellular and Molecular Responses to Alkylation Damage in DNA |
|
|
757 | (24) |
|
|
|
|
|
|
|
757 | (3) |
|
The E. coli Adaptive Response: Translating Methyl DNA Adducts into a Transcriptional Signal |
|
|
760 | (6) |
|
Cellular Responses to O6MeG |
|
|
766 | (5) |
|
Cellular Responses to 3MeA |
|
|
771 | (4) |
|
Genome-Wide Analysis of Responses to Alkylating Agents |
|
|
775 | (1) |
|
|
|
776 | (5) |
|
|
|
776 | (5) |
|
Damage Signals Triggering the Escherichia coli SOS Response |
|
|
781 | (22) |
|
|
|
|
|
781 | (1) |
|
|
|
781 | (3) |
|
Structure-Function of the LexA Protein Family |
|
|
784 | (2) |
|
RecA Protein-DNA Interactions and LexA Self-Cleavage |
|
|
786 | (3) |
|
Role of DNA Damage in Inducing the E. coli SOS Response |
|
|
789 | (2) |
|
Upregulation of DNA Repair and DNA Damage Tolerance Under the SOS Response |
|
|
791 | (4) |
|
After the Damage is Repaired: Turning off the SOS Response and the Return to Normalcy |
|
|
795 | (2) |
|
Concluding Remarks and Future Perspectives |
|
|
797 | (6) |
|
|
|
798 | (5) |
|
Recognition of DNA Damage as the Initial Step of Eukaryotic Checkpoint Arrest |
|
|
803 | (24) |
|
|
|
|
|
803 | (1) |
|
Early Studies Characterizing Checkpoint Triggering Damage and Sensor Proteins |
|
|
804 | (1) |
|
The ATM Protein is a Kinase and a Putative Damage Sensor |
|
|
805 | (2) |
|
The ATR Protein and its Targeting Subunit |
|
|
807 | (1) |
|
PCNA- and RFC-like Clamp and Clamp Loader Complexes Function as Damage Sensors |
|
|
808 | (2) |
|
Crosstalk Between Sensors |
|
|
810 | (1) |
|
The MRN Complex Plays a Role in Checkpoint Arrests |
|
|
811 | (1) |
|
Synopsis: Independent But Communicating Sensors Are Linked By Common Requirements |
|
|
812 | (1) |
|
The Generation of a Transducible Signal |
|
|
812 | (2) |
|
|
|
814 | (1) |
|
|
|
815 | (1) |
|
Adaptation and Cell Cycle Restart |
|
|
816 | (11) |
|
|
|
818 | (9) |
|
Responses to Replication of DNA Damage |
|
|
827 | (14) |
|
|
|
|
|
|
|
827 | (1) |
|
How do Cells Deal with a Damaged Template During DNA Replication? |
|
|
828 | (2) |
|
|
|
830 | (7) |
|
Replication-Related Genome Instability |
|
|
837 | (4) |
|
|
|
837 | (4) |
| Index |
|
841 | |
Lisainfo e-raamatute kohta