Radical and Radical Ion Reactivity in Nucleic Acid Chemistry (Wiley Series of Reactive Intermediates in Chemistry and Biology)

469 Pages·2009·24.26 MB·English

by  M. Greenberg

RADICAL AND RADICAL
ION REACTIVITY
IN NUCLEIC
ACID CHEMISTRY
Wiley Series of Reactive Intermediates in
Chemistry and Biology
StevenE.Rokita,SeriesEditor
Quinone Methides
Edited by Steven E. Rokita
Radical and Radical Ion Reactivity inNucleic Acid Chemistry
Edited by Marc M.Greenberg
RADICAL AND RADICAL
ION REACTIVITY
IN NUCLEIC
ACID CHEMISTRY
Edited by
MARC M. GREENBERG
Copyright(cid:1)2009byJohnWiley&Sons,Inc.Allrightsreserved
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LibraryofCongressCataloging-in-PublicationData:
Radicalandradicalionreactivityinnucleicacidchemistry/editor,MarcM.
Greenberg.
p.cm.
Includesindex.
ISBN978-0-470-25558-2(cloth)
1. Nucleicacids–Effectofradiationon. 2. DNA. 3. Ionization. 4. Free
radicals(Chemistry) I. Greenberg,MarcM.
QP620.R3372009
5720.33–dc22
2009009770
PrintedintheUnitedStatesofAmerica
10987654321
CONTENTS
Preface to Series vii
Introduction ix
Contributors xi
1. TheoreticalModelingof Radiation-InducedDNA Damage 1
AnilKumarandMichaelD.Sevilla
2. Radical Reaction Pathways Initiated by DirectEnergyDeposition
inDNA by IonizingRadiation 41
WilliamA.Bernhard
3. Chemical Reactions ofthe Radical Cations ofNucleobases in
Isolated and Cellular DNA. Formation ofSingle-Base Lesions 69
JeanCadet,ThierryDouki,DidierGasparutto,Jean-LucRavanat,and
J.RichardWagner
4. Reactivityof Nucleic Acid Sugar Radicals 99
ChryssostomosChatgilialoglu
5. Pyrimidine Nucleobase Radical Reactivity 135
MarcM.Greenberg
6. Reactivityof 5-Halopyrimidines inNucleicAcids 163
RyuTashiroandHiroshiSugiyama
v
vi CONTENTS
7. Kinetics ofLong-Range Oxidative Electron Transfer
ThroughDNA 191
KiyohikoKawaiandTetsuroMajima
8. Radical IntermediatesDuringReductive Electron Transfer
ThroughDNA 211
RejiVargheseandHans-AchimWagenknecht
9. Low-Energy Electron Interactionwith DNA:Bond Dissociation
and Formation ofTransient Anions, Radicals,and Radical Anions 239
L(cid:1)eonSanche
10. Electronic-AffinicRadiosensitizers 295
PeterWardman
11. Reactionsof Reactive Nitrogen SpeciesandCarbonate
Radical Anionswith DNA 325
VladimirShafirovich,ConorCrean,andNicholasE.Geacintov
12. Principlesand Applicationsof Electrochemical
Oxidation of Nucleic Acids 357
H.HoldenThorpandJulieM.Sullivan
13. DNA DamageDue to Diradical-Generating Cyclizations 389
SeanM.Kerwin
14. DNA Damageby Phenoxyl Radicals 421
RichardA.Manderville
Index 445
PREFACE TO SERIES
Moststablecompoundsandfunctionalgroupshavebenefitedfromnumerousmono-
graphsandseriesdevotedtotheiruniquechemistry,andmostbiologicalmaterialsand
processeshavereceivedsimilarattention.Chemicalandbiologicalmechanismshave
also been the subject of individual reviews and compilations. When reactive inter-
mediates are given center stage, presentations often focus on the details and
approaches of one discipline despite their common prominence in the primary
literature of physical, theoretical, organic, inorganic, and biological disciplines.
The Wiley Series on Reactive Intermediates in Chemistry and Biology is designed
tosupplyacomplementaryperspectivefromcurrentpublicationsbyfocusingeach
volumeonaspecificreactiveintermediateandendowingitwiththebroadestpossible
contextandoutlook.Individualvolumesmayservetosupplementanadvancedcourse,
sustain a special topics course, and provide a ready resource for the research
community. Readers should feel equally reassured by reviews in their speciality,
inspiredbyhelpfulupdatesinalliedareasandintriguedbytopicsnotyetfamiliar.
This series revelsin the diversityofits perspectivesand expertise. Where some
books drawstrength from their focused details, this series draws strength from the
breadth of its presentations. The goal is to illustrate the widest possible range of
literaturethatcoversthesubjectofeachvolume.Whenappropriate,topicsmayspan
theoreticalapproachesforpredictingreactivity,physicalmethodsofanalysis,strate-
gies for generating intermediates, utility for chemical synthesis, applications in
biochemistry and medicine, impact on the environmental, occurrence in biology,
andmore.Experimentalsystemsusedtoexplorethesetopicsmaybeequallybroadand
rangefromsimplemodelstocomplexarraysandmixturessuchasthosefoundinthe
finalfrontiersofcells,organisms,earth,andspace.
vii
viii PREFACETOSERIES
Advancesinchemistryandbiologygainfromamutualsynergy.Asnewmethods
aredevelopedforonefield,theyareoftenrapidlyadaptedforapplicationintheother.
Biologicaltransformationsandpathwaysofteninspireanalogousdevelopmentofnew
procedures in chemical synthesis, and likewise, chemical characterization and
identificationoftransientintermediatesoftenprovidethefoundationforunderstand-
ingthebiosynthesisandreactivityofmanynewbiologicalmaterials.Whileindividual
chaptersmaydrawfromasingleexpertise,therangeofcontributionscontainedwithin
eachvolumeshouldcollectivelyofferreaderswithamultidisciplinaryanalysisand
exposuretothefullrangeofactivitiesinthefield.Asthisseriesgrows,individualized
compilationsmayalsobecreatedthroughelectronicaccesstohighlightaparticular
approachorapplicationacrossmanyvolumesthattogethercoveravarietyofdifferent
reactiveintermediates.
Interestinstartingthisseriescameeasily,butthecreationofeachvolumeofthis
series required vision, hard work, enthusiasm, and persistence. I thank all of the
contributorsandeditorswhograciouslyacceptedandwillacceptthechallenge.
STEVENE.ROKITA
Universityof Maryland
INTRODUCTION
Morethanacenturyago,observationswerereportedinaperiodoflessthanfiveyears
fromdistinctfieldsthatwouldcomprisealargeportionofthebasisofradicalmediated
DNA damage. X-rays were discovered in 1895 and used to treat tumors shortly
thereafter.Inaddition,bytheturnofthetwentiethcenturytheFentonreactionwas
reportedandin1900Gombergproposedtheformationofthefirstcarbon-centered
radical.Theseseeminglydisconnectedreportswereultimatelydeterminedtooverlap
significantly.X-rayswerefoundtokilltumorcellsbyoxidativelydamagingDNA.
Hydroxylradical,whichisproducedfromhydrogenperoxideintheFentonreaction,
wasfoundtobeaprimaryreactivespeciesresponsibleforDNAdamagemediatedby
gammaradiolysis.Finally,theconnectionsarecompletedbytheformationofradicals
inDNA.Thecarbon-centered(andother)DNAradicalsareproducedfromhydroxyl
radicalbyhydrogenatomabstraction,aswellasbyadditiontop-bonds.
Thecomplexityofthischemistrybecomesimmediatelyapparentuponconsidering
thesizeandheterogeneityofDNA,aswellasthevarietyofexperimentalconditions
(e.g., O , redox active metal ions, hydrogen atom donors) under which damage is
2
induced.
DespitethecomplexnatureofoxidativeDNAdamage,abroadrangeofscientists
usingavarietyofphysicalandanalyticalmethodshavemadesignificantcontributions
toourunderstandingofthischemistryduringthelatterhalfofthetwentiethcentury.
ClemensvonSonntag,aleaderinthisfield,summarizedmuchofthisresearchinhis
seminal book The Chemical Basis of Radiation Biology (1987). By using ionizing
radiationinconjunctionwithvarioustechniquessuchasmassspectrometryandEPR
spectroscopy,scientistswereabletoidentifyproducts,observereactiveintermediates,
and proffer mechanisms of nucleic acid damage. Recent contributions describing
significantadvancesincomputationalaspectsofradiationdamage,aswellthedirect
ix
x INTRODUCTION
effectsofionizingradiation,theroleofreactivespeciesotherthanhydroxylradical
producedbyionizingradiation,theeffectsofelectronaffinicradiosensitizingagents
on DNA radical chemistry, and the exciting realization of the role of low energy
electronsinDNAdamage,aredescribedinthisbook.
InvestigationsinwhichionizingradiationisusedtoinitiateDNAdamagefacethe
limitationthattheylackcontroloverwhichreactiveintermediatesareproducedorthey
cannot control where nucleic acids are damaged. The advent of solid phase oligo-
nucleotides synthesis, modern mass spectrometry methods capable of analyzing
biopolymersdirectly(e.g.,MALDI-TOFMSandESI-MS),andtheassimilationof
biochemicaltechniquessuchasgelelectrophoresisandtheutilizationofnucleicacid
modifyingenzymesprovidedchemistswiththewherewithaltoprobeoxidativeDNA
damagewithgreaterprecision.Byutilizingthesetoolsinconjunctionwithchemical
synthesisofoligonucleotidescontainingmodifiednucleotides,chemistswereableto
simplify studies on nucleic acid damage and in the process uncover mechanistic
complexitiesandunrecognizedreactionpathways.Inaddition,theapplicationofthese
andotherstate-of-the-arttechniquesfacilitatedelucidatingthepathwaysforelectron
transferinDNAthatcanbeinitiateddirectlyorindirectlybyionizingradiation,aswell
as the utilization of DNA damage as a means for understanding protein–DNA
interactions, the mechanisms of drugs and other species that target DNA, and the
utilizationofDNAdamageasachemicalsensor.Expertsontherespectivetopicsalso
reviewadvancesineachoftheseareasinthiscompilation.
Iamgratefultoallofthecontributorstothisbook.Theirresearchandthatofothers
described within have provided a deeper understanding of this biologically and
technologicallysignificantareaofscienceandhavealsoprovidedthebasisforfuture
investigationsandapplicationsofradicalsinnucleicaciddamageingeneral.Finally,I
wanttothankProfessorStevenRokitaforhavingthevisionandmotivationtoestablish
Reactive Intermediates in Chemistry and Biology, as well as for inviting me to
participateinthisproject.
MARCM.GREENBERG
JohnsHopkinsUniversity