Oxidative Damage to Nucleic Acids (Molecular Biology Intelligence Unit)

244 Pages·2007·15.56 MB·English

by  Mark D. Evans

MOLECUlAR BIOWGY
INTELLIGENCE
UNIT
Oxidative Damage
to Nucleic Acids
Mark D. Evans, B.Sc., Ph.D.
Radiation and Oxidative StressGroup
DepartmentofCancerStudies and MolecularMedicine
RKCSB, Leicester RoyalInfirmary
UniversityofLeicester
Leicester, U.K.
Marcus S. Cooke, B.Sc., M.Sc., Ph.D.
Department ofCancerStudies and Molecular Medicine
and
Department ofGenetics
UniversityofLeicester
Leicester, U.K.
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OXIDATIVE DAMAGE TO NUCLEIC ACIDS
MolecularBiology Intelligence Unit
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LibraryofCongress Cataloging-ia-PubilcationData
Oxidativedamagetonucleicacids1[editedby]MarkD. Evans,MarcusS.Cooke.
p.;em.-- (Molecularbiologyintelligenceunit)
Includes bibliographicalreferencesand index.
ISBN-13:978-0-387-72973-2(a1k.paper)
1. Nucleicacids-Oxidation.2. DNArepair. 3. Chemicalmutagenesis. I.Evans,MarkD. (Mark
Dennis), 1962- II.Cooke,Marcus S.III. Series:Molecularbiologyintelligence unit(Unnumbered)
[DNLM: 1. DNADamage. 2. OxidativeStress.3. Antioxidants-vtherapeuticuse.4. DNARepair
Enzymes. 5. DNARepair. QU477 0982007]
QP620.0952007
611'.01816--dc22
2007024908
About the Editors...
MARK D. EVANS is a non-clinical
lecturer in the Department ofCancer Studies
and Molecular Medicine at the University of
Leicester, U.K. His main researchinterestsare
in the areasofDNAoxidation and repairand
the pathological roles of DNA oxidation in
malignant and non-malignant disease. He
obtained his B.Sc. (Hons) in Applied Bio
chemistry from Brunei University, Uxbridge
U.K.HegraduatedwithaPh.D.,intheareaof
cigarettesmoke-induced protein damage and
emphysema, from Louisiana State University,
Baton Rouge working in The Biodynamics
Institute and Department of Biochemistry
undertheguidanceofProfessorWilliamA Pryor.
MARCUSS.COOKEisaseniorlecturer
with a joint appointment between the De
partment ofCancer Studies and Molecular
Medicine and the Department ofGenetics,
at the University of Leicester. The role of
genotoxicologyin the pathogenesis ofdisease
is the central theme in his researchprogram,
focussed primarily upon free radical mecha
nismsofcellulardamage, particular oxidative
DNAdamageandrepair.HeobtainedhisB.Sc.
(Hons) in Biomedical Sciences at Liverpool
Polytechnic, before moving to the University
ofLeicesterforhisM.Sc.inMolecularPathol
ogyandToxicology, and then hisPh.D. in ul
tra-violetradiation and freeradicalbiochemis
try.HewasappointedaFellowofthe Institute
ofBiomedicalSciencein 1997, and in 2004
becameaChartered Scientist.
MDE wouldlike to dedicate this book to hisfamily,
relations andfriends ofthefamily-past, presentandfUture.
MSC wouldlike to dedicate this book to Emily andEvie.
r.======CONTENTS================:::::;l
Preface xv
1. OxidativelyGeneratedDamageto CellularDNA:
MechanisticAspects 1
Jean Cadet, ThierryDouki, CarineBadouard,AlainFavier
andJean-LucRavanat
Hydroxyl Radical-Mediated OxidationofThymine 2
DegradationPathwaysofPurine Basesby'OH Radical 4
SingletOxygen OxidationofGuanine 6
Halogenation ReactionsofNucleobasesbyHOCI 7
SecondaryRadicalOxidation Reactions
of8-oxo-7,8-dihydroguanine 8
2. ChlorinationandNitrationofDNAandNucleic AcidComponents 14
ClareL.Hawkins, DavidI Pattison, MatthewWhiteman
andMichaelj. Davies
Chlorination 16
Nitration 21
3. Preventionofthe MutagenicityandCytotoxicity
ofOxidizedPurineNucleotides 40
YusakuNakabeppu, MehrdadBehmanesb, Hiroo Yamaguchi,
Daisuke YoshimuraandKunihikoSakumi
OxidationofFreeNucleotides and Their Mutability 40
RemovalofOxidized Nucleotides bySanitization
ofNucleotidePools 42
Mutagenesisand CarcinogenesisCaused bytheAccumulation
ofOxidized Nucleotides and Prevention byMTHI 46
Cellular DysfunctionCaused bytheAccumulationofOxidized
Nucleotides and ItsPrevention byMTH1 46
NeuronalAccumulationofOxidizedNucleotides Causes
Neurodegeneration, Suppression byMTHI 48
Oxidative DeaminationofNucleotides
and ItsBiologicalConsequences 48
4. NucleotideIncisionRepair:AnAlternativeand Ubiquitous
Pathwayto HandleOxidativeDNADamage 54
Sophie Couoe-Prioat,AlexanderA.Isbcbenko,JacquesLaval
andMuratSaparbaev
FreeRadicalSpeciesand Oxidative Damage ofDNA 56
APEndonucleasesInvolvedinthe NucleotideIncision
RepairPathway 56
Substrate SpecificityofNIREndonucleases
andTheirPhysiologicalRelevance 58
Structureand 3'-5' ExonucleaseActivityofAPEndonucleases 60
5. OGG1: From StructuralAnalysisto the KnockoutMouse 67
ArneKlungland,JonK LaerdahlandTorbjemRognes
CloningofOGG1 '" 68
SubstrateSpecificityofOGG1 70
OGG1Structure , 70
OGG1CatalyticMechanism 73
OGGIMutants 74
BackupActivitiesforOGG1 76
OGG1Orthologs 76
6. Processingof3'-EndModifiedDNAStrandBreaksInduced
byOxidativeDamage 81
JasonL.Parsons, EmmaBoswellandGrigoryL.Dianov
Formationof"Damaged" DNA3'-Ends 82
RepairofDNASingleStrand BreaksInduced bythe Base
ExcisionRepairPathway 82
APEndonuclease 1(APEI) 84
Polynucleotide Kinase(PNK) 85
Tyrosyl-DNAPhosphodiesterase 1(TdpI) 85
Aprataxin 86
Polymorphisms ofProteins Involvedinthe Processingof3'-End
Modified DNAStrandBreaks 86
7. OxidativeDamageandPromoterFunction 91
DavidMitchellandRitaGhosh
NonrandomInductionofOxidative Damage
inPromoterRegions 92
CisEffectsofOxidative Damageon PromoterFunction 93
TransEffectsofOxidative Damageon PromoterFunction 95
8. OxidativeDNADamageandTelomereShortening 100
TorstenRichterandThomas vonZglinicki
Telomere Structure 100
Telomeresand DNARepair 102
Telomere Shorteningand DNADamage 102
TelomeresAreVulnerable to OxidativeStress-Induced
Single-Strand Breaks 103
Telomere-SpecificDeficiencyofSSB Repair 105
PossibleMechanisms ofStress-DependentTelomere Shortening 106
9. OxidativeDamageand Repair in the MitochondrialGenome 109
LeneJuelRasmussenandKeshavK Singh
RepairofOxidatively-Damaged DNAinthe Nucleus 110
RepairofOxidatively-Modified DNAinMitochondria 114
Imbalanced RepairinMitochondria 117
Mitochondria-MediatedMutagenesis 117
Mitochondrial Dysfunctionand HumanDisease 117
10. TheRoleofOxidativeDamagetoNucleicAcids
in the PathogenesisofNeurologicalDisease 123
V.PrakashReddy,AyseBeyaz, GeorgePerry, MarcusS.Cooke,
LawrenceM. SayreandMarkA.Smith
OxidativeStressand FreeRadicalSpecies 124
OxidativeStressInvolvingAdvancedGlycationEnd Products
(AGEs)andAdvancedLipidPeroxidation End Products (ALEs) 128
MarkersofNucleicAcidDamageinAD 132
Mitochondrial DNADamage 134
DNARepairinAD 134
11. NucleicAcidOxidationand the Pathogenesis
ofCardiovascularDiseases 141
MariaGraziaAndreassi
PathogenesisofAtherosclerosis.......................................................... 142
Genetic Instabilityand OxidativelyDamaged DNA
inAtherosclerosis 145
12. Oxidative DNADamageand Carcinogenesis 153
RyszardGlinski, MarekFoksinskiandBarbara Tudek
Accumulation of8-0HGuainCancerPatients 154
OxidativeDNADamageRepair,Mutagenesisand Carcinogenesis 156
Aging,Cancerand OxidativeDNA Damage 160
RoleofInflammationinROS Generationand OxidativeDNA
Damage-Associationwith Cancer Development 161
13. ThePhysiologicalandPathological RolesofOxidative
Damage to DNA in Relation to LifeStage 167
AlbertoIzzotti
EarlyLifeStages:IntrauterineLife 169
TheFoetus-NewbornTransition 171
Intermediate LifeStages 173
LateLifeStages 174
14. Analysisof8-Hydroxy-2'-DeoxyguanosineasaMarkerofOxidatively
DamagedDNAin Relation to Carcinogenesis andAging 178
H. Kasai, T.Hirano, K Kawai, Y.Tsurudome, H. Itoh, D.Himeji
andT.Horiuchi
Methods forMeasuring8-0H-dG inDNA 179
Formation of8-0H-dG inDNAofAnimal Organ or Cultured
CellDNAduringAgingand byTreatmentwith Oxidative
Stress-InducingCarcinogens 180
ClinicalAnalysisof8-0H-dG in HumanDNA 180
Analysisofthe 8-0H-dG RepairSystem 180
AnalysisofUrinary 8-0H-dG 181
Urinary 8-0H-dG Levelsin CancerPatientsand Cancer
High-Risk Groups 184
15. OxidativelyDamagedDNAand Inflammation 188
PeterC DedonandMarita C Barth
ChemicalMediators ofInflammation 189
Nitrosative DeaminationofDNA 190
OxidationofDNAbyPeroxynitrite and Nitrosoperoxycarbonate 192
ReactionsofDNAwith Endogenous ElectrophilesArising
from Oxidation 197
Oxidative DNADamageasaSourceofDNA
Adduct-FormingElectrophiles 198
PuttingItAllTogether: DNABiomarkers
ofInflammationinVivo 200
16. TheRoleofAntioxidantsin the PreventionofOxidative
Damageto NucleicAcids 207
PeterMetlerandSteffenLoft
Evaluation ofAntioxidantInterventionStudies 209
EffectofAntioxidantSupplementationon Oxidative
DNADamage inWBC 210
EffectofAntioxidantSupplementationon 8-0HdG
LevelsinUrine 214
Index 225
EDITORS
r;:=::============== =================:::;-]
MarkD. Evans
Radiation and Oxidative Stress Group
Department ofCancer Studies and MolecularMedicine
RKCSB, Leicester Royal Infirmary
UniversityofLeicester
Leicester, U.K.
Email: [email protected]
Preface
Marcus S. Cooke
Department ofCancer Studies and MolecularMedicine
and
DepartmentofGenetics
UniversityofLeicester
Leicester, U.K.
Email: [email protected]
Preface, Chapter10
~~~=CONTroBUTORS~~~~
Maria GraziaAndreassi MehrdadBehmanesh
CNRInstituteofClinicalPhysiology DepartmentofGenetics
G. PasquinucciHospital School ofSciences
Massa,Italy TarbiatModarresUniversity
Email:[email protected] Tehran,Iran
Chapter11 Chapter3
CarineBadouard AyseBeyaz
DepartementdeRechercheFondamentale DepartmentofChemistry
surlaMatereCondensee UniversityofMissouri-Rolla
Laboratoire"LesionsdesAcides Rolla,Missouri, U.S.A.
Nucleiques" Chapter10
Grenoble, France
Chapter1 EmmaBoswell
Medical ResearchCouncil
MaritaC.Barth RadiationandGenomeStabilityUnit
BiologicalEngineeringDivision Harwell, Oxfordshire,U.K.
and Chapter6
CenterforEnvironmentalHealthSciences
MassachusettsInstituteofTechnology
Cambridge,Massachusetts, U.S.A.
Chapter15