The Chemical Biology of Nucleic Acids PDF
Preview The Chemical Biology of Nucleic Acids
The Chemical Biology of Nucleic Acids Editedby GU¨NTERMAYER StrathclydeInstituteforPharmacyandBiologicalSciences, UniversityofStrathclyde,Glasgow,UK A John Wiley and Sons, Ltd., Publication The Chemical Biology of Nucleic Acids The Chemical Biology of Nucleic Acids Editedby GU¨NTERMAYER StrathclydeInstituteforPharmacyandBiologicalSciences, UniversityofStrathclyde,Glasgow,UK A John Wiley and Sons, Ltd., Publication Thiseditionfirstpublished2010 (cid:2)2010JohnWiley&Sons,Ltd Registeredoffice JohnWiley&SonsLtd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UnitedKingdom Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformationabouthowtoapplyforpermissiontoreusethe copyrightmaterialinthisbookpleaseseeourwebsiteatwww.wiley.com. TherightoftheauthortobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewiththeCopyright,DesignsandPatents Act1988. 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LibraryofCongressCataloging-in-PublicationData Thechemicalbiologyofnucleicacids/editor,Gu¨nterMayer. p. ; cm. Includesbibliographicalreferencesandindex. ISBN978-0-470-51974-5(cloth) 1. Nucleicacids. I. Mayer,Gu¨nter,1972– [DNLM: 1. NucleicAcids—chemistry. 2. NucleicAcids—physiology. 3. NucleicAcids—therapeuticuse. QU58C51652010] QP620.C442010 572.8—dc22 2010000254 AcataloguerecordforthisbookisavailablefromtheBritishLibrary. ISBN:978-0-470-51974-5 Setin10/12ptTimesbyIntegraSoftwareServicesPvt.Ltd.,Pondicherry,India PrintedandboundinGreatBritainbyCPIAntonyRowe,Chippenham,Wiltshire. Contents Foreword vii Preface ix ListofContributors xi 1 ChemicalSynthesisofModifiedRNA 1 ClaudiaHo¨bartnerandFalkWachowius 2 ExpansionoftheGeneticAlphabetinNucleicAcidsbyCreating NewBasePairs 39 IchiroHiraoandMichikoKimoto 3 ChemicalBiologyofDNAReplication:ProbingDNAPolymeraseSelectivity MechanismswithModifiedNucleotides 63 AndreasMarx 4 NucleicAcid-templatedChemistry 73 MichaelOberhuber 5 ChemicalBiologyofPeptideNucleicAcids(PNAs) 103 PeterE.Nielsen 6 TheInteractionsofSmallMoleculeswithDNAandRNA 115 YunXie,VictorK.TamandYitzhakTor 7 TheArchitecturalMotifsofFoldedRNAs 141 Vale´rieFritschandEricWesthof 8 GenesisandBiologicalApplicationsofLockedNucleicAcids(LNAs) 175 HarleenKaurandSouvikMaiti 9 SmallNon-codingRNAinBacteria 199 SabineBrantl 10 MicroRNA-guidedGeneSilencing 223 GunterMeister 11 NucleicAcid-basedTherapies 233 BrittaHoehnandJohnJ.Rossi vi Contents 12 InnateImmuneRecognitionofNucleicAcids 261 StefanBauer 13 Light-responsiveNucleicAcidsfortheSpatiotemporalControl ofBiologicalProcesses 279 AlexanderHeckelandGu¨nterMayer 14 DNAMethylation 307 AlbertJeltschandRenataZ.Jurkowska 15 FrameworksforProgrammingRNADevices 323 MaungNyanWin,JoeC.LiangandChristinaD.Smolke 16 RNAasaCatalyst:TheDiels–AlderaseRibozyme 339 AndresJa¨schke 17 EvolvinganUnderstandingofRNAFunctionbyInVitroApproaches 355 QingWangandPeterJ.Unrau 18 TheChemicalBiologyofAptamers:SynthesisandApplications 377 Gu¨nterMayerandBernhardWulffen 19 NucleicAcidsasDetectionTools 401 JeffreyC.F.Lam,SergioAguirreandYingfuLi 20 BacterialRiboswitchDiscoveryandAnalysis 433 TylerD.AmesandRonaldR.Breaker Index 455 Foreword ChemistshaveplayedakeyrolenotonlyinestablishingthechemicalstructureofDNAandRNAbutalsoin helping to understand their structure–function relationships. This fascination has continued over the years and, as the present book demonstrates, is unabated. The many chapters are great testimony to the fruitful interplay in nucleic acid chemistry and biology. As chemists have continued over the years to modify the structureandarchitectureofDNAandRNAforanevenbetterinsightintotheirbiologicalfunctions,Nature haslatelyprovidednewchallengesbydisclosingsomeunanticipatednovelstructuresandpathways.These newinsightsintoNatureposequestionswherechemistryhelpstoobtainadeeperunderstanding. Even though the chemistry of nucleic acids has been described over the years in many textbooks and reviews, the chapters in this book describe the efforts and successes achieved in the last few years in combination with more recent developments. Hence this book comprises an appreciated update review of thechemicalbiologyofnucleicacidsasitstandstoday. Thebookcoversawidescope,withchaptersonspecifictopicswrittenbyexpertsintheparticulararea. GiventhenewhorizonsontheroleofRNAwhichwehaveexperiencedoverrecentyears,itisnotsurprising that several chapters describe RNA chemistry as an essential component for the deeper analysis of these phenomena.ThechemicalsynthesisofmodifiedRNAis,ofcourse,fundamentalandisrightlydescribedat the beginning. RNA occurs in a surprisingly wide range of architectural motifs commensurate with the multitudeoffunctionsasadetailedaccountdescribes.Theversatilityofstructuralmotifsisalsoapparentin thenaturallyoccurringriboswitches.Theseareresponsibleforthecontroloftranslationortranscriptionby bindingofsmallcellularmetabolites.Thisareaisstillverymuchinfluxandnovelriboswitchesarebeing discovered every year, supporting RNA as an important regulator for gene expression. MicroRNAs are a noveltypeofsmallRNAswhosemechanismofregulationofgeneexpressionisstillunderinvestigation.So far,chemistryhasnotgenerallybeenappliedtothese,eventhoughformedicalapplicationsthislooksrather enticing.Thefunctionsofsmallnon-codingRNAsinbacteriaareattractingincreasingattentionanddeserve thein-depthreviewpresented.Thisshouldmakechemistsawareofafieldwhichhasbeenneglectedbythem sofar. RNAandDNAcanactuallysharecertainfunctions.Thisisseeninthecatalyticpropertieswhichbothcan adoptincatalyticRNA(ribozymes)andDNAzymes,whichbythemselvesoccurinavarietyofarchitectures. AptamerscanalsoconsistofRNAorDNAtobindproteinsandothermoleculesextremelyspecifically.The structures with these properties have been obtained by in vitro selection from random sequences where selectivepressureplaysanimportantroleinsamplingthesequencespace.Theexamplesprovideddemon- strateagainthearchitecturaland,withit,thefunctionalversatilityofRNAandDNA.Asreviewedinseveral chapters,theseinturnrepresentexcellentopportunitiesformodulationbychemicalderivatization. Besides riboswitches, small molecules bind to RNA also in a different setting, such as to the ribosomal RNA,whereaminoglycosidesaretheparadigmandwheretheyexertantimicrobialeffects.Thefundamental viii Foreword featuresplayingaroleinsuchinteractionsofsmallmoleculeswithnucleicacidsingeneralisaninteresting subject. Sugar-andbase-modifiednucleotideshavebeenasubjectofstudyformanyyears,yetnovelaspectsare still being explored. One example is the use of such modified nucleotides to study the selectivity of DNA polymerases. Another is the creation of new base pairs to expand the scope of the genetic alphabet by incorporation into DNA or RNA by replication and transcription. Of the sugar-modified nucleotides, the locked nucleic acids (LNAs) have found wide application because of their strong binding to RNA. This propertymakesthemmostsuitableforinteractionwithmRNAandmicroRNAsforinterferencewithgene expression.Anentirelydifferentanalogue isthe peptidenucleicacids (PNAs),where thephosphateback- boneandthedeoxyribosearereplacedbyamidelinkages.Eventhoughthisisadrasticchangeinstructure, thePNAsstillhybridizefavourablywithDNAandRNAbutare,ofcourse,completelyresistanttonucleases. TheyrepresentverypowerfulDNAmimicswithinterestingproperties. Thepotentialofnucleicacidsfortherapyisawell-studiedareawherevariousstrategiesarebeingexplored andbeingexaminedinclinicaltrials.Thereishighpotentialinthisappliedareaandwelook forwardtoa generalbreakthroughfortheapprovalofdrugs. Insummary,thiscollectionofreviewsistestimonytothefruitfulrolethatchemistscanplayinhelpingto understand structure–function relationships in nucleic acids and their mechanisms of action. Recent years haveprovidedbigsurprises,particularlyinthefieldofRNA,whichindicatesthatthefieldiswideopenwith lotsofopportunitiesandchallenges. FritzEckstein Go¨ttingen 2010
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