Radical and Radical Ion Reactivity in Nucleic Acid Chemistry (Wiley Series of Reactive Intermediates in Chemistry and Biology) PDF
Preview Radical and Radical Ion Reactivity in Nucleic Acid Chemistry (Wiley Series of Reactive Intermediates in Chemistry and Biology)
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 PublishedbyJohnWiley&Sons,Inc.,Hoboken,NewJersey PublishedsimultaneouslyinCanada Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmittedinanyformorby anymeans,electronic,mechanical,photocopying,recording,scanning,orotherwise,exceptaspermitted underSection107or108ofthe1976UnitedStatesCopyrightAct,withouteitherthepriorwritten permissionofthePublisher,orauthorizationthroughpaymentoftheappropriateper-copyfeetothe CopyrightClearanceCenter,Inc.,222RosewoodDrive,Danvers,MA01923,(978)750-8400,fax(978) 750-4470,oronthewebatwww.copyright.com.RequeststothePublisherforpermissionshouldbe addressedtothePermissionsDepartment,JohnWiley&Sons,Inc.,111RiverStreet,Hoboken,NJ07030, (201)748-6008,fax(201)748-6008,oronlineathttp://www.wiley.com/go/permission. LimitofLiability/DisclaimerofWarranty:Whilethepublisherandauthorhaveusedtheirbesteffortsin preparingthisbook,theymakenorepresentationsorwarrantieswithrespecttotheaccuracyor completenessofthecontentsofthisbookandspecificallydisclaimanyimpliedwarrantiesof merchantabilityorfitnessforaparticularpurpose.Nowarrantymaybecreatedorextendedbysales representativesorwrittensalesmaterials.Theadviceandstrategiescontainedhereinmaynotbesuitablefor yoursituation.Youshouldconsultwithaprofessionalwhereappropriate.Neitherthepublishernorauthor shallbeliableforanylossofprofitoranyothercommercialdamages,includingbutnotlimitedtospecial, incidental,consequential,orotherdamages. Forgeneralinformationonourotherproductsandservicesorfortechnicalsupport,pleasecontactour CustomerCareDepartmentwithintheUnitedStatesat(800)762-2974,outsidetheUnitedStatesat(317) 572-3993orfax(317)572-4002. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprint maynotbeavailableinelectronicformats.FormoreinformationaboutWileyproducts,visitour websiteatwww.wiley.com. 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
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