From Nucleic Acids Sequences to Molecular Medicine PDF
Preview From Nucleic Acids Sequences to Molecular Medicine
RNA Technologies Forfurther volumes: http://www.springer.com/series/8619 . Volker A. Erdmann (cid:129) Jan Barciszewski Editors From Nucleic Acids Sequences to Molecular Medicine Editors Prof.Dr.VolkerA.Erdmann Prof.Dr.JanBarciszewski FreeUniversityBerlin PolishAcademyofSciences InstituteofChemistry/Biochemistry InstituteofBioorganicChemistry Thielallee63 Z.Noskowskiego12/14 14195Berlin 61-704Poznan Germany Poland [email protected] [email protected] ISBN978-3-642-27425-1 ISBN978-3-642-27426-8(eBook) DOI10.1007/978-3-642-27426-8 SpringerHeidelbergNewYorkDordrechtLondon LibraryofCongressControlNumber:2012940711 #Springer-VerlagBerlinHeidelberg2012 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerpts inconnectionwithreviewsorscholarlyanalysisormaterialsuppliedspecificallyforthepurposeofbeing enteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework.Duplication ofthispublicationorpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthe Publisher’s location, in its current version, and permission for use must always be obtained from Springer.PermissionsforusemaybeobtainedthroughRightsLinkattheCopyrightClearanceCenter. ViolationsareliabletoprosecutionundertherespectiveCopyrightLaw. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. While the advice and information in this book are believed to be true and accurate at the date of publication,neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityfor anyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,with respecttothematerialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Nucleic Acids Meet Human Genetic Medicine With this volume of the series RNA Technologies, we aim to cover current and important developments in RNA chemistry, RNA biology, and the application of RNAmoleculesinmolecularmedicine. Cellular gene expression is based on several levels of information. First the sequenceofthecanonicaladenine,cytosine,guanosine,andthyminebasesinDNA encodes for the primary structures of proteins through their specific base triplet arrangements.The“CentralDogmaofMolecularBiology”taughtusthattheDNA is transcribed into RNAs and the protein-coding messenger RNA genes are then translated into proteins by ribosomes. For its function the ribosomes are directly dependent upon noncoding RNAs such as ribosomal RNAs, tRNAs, and small nuclearRNA.ItisnowevidentthatRNA,ingeneexpression,functionsfarbeyond the established roles of these RNAs, for example, in RNA splicing and editing, telomere maintenance, protein secretion, small-molecule sensing, and reaction catalysis. Thus, RNA molecules play a key role in several fundamental cellular processes,servingasacarrierofgeneticinformationand,veryimportantly,alsoas itsregulator. Inhumaneukaryoticcellsonlyca.1.8%ofthegenomicDNAistranscribedinto mRNAs, while the remaining 98.2% represents the so-called noncoding DNA sequences.Asdiscoveredoverthelast20years,alargeamountofthisnoncoding DNArepresentsactuallynoncodingRNA.TheimportantroleofnoncodingRNAs in cellular processes has recently become more and more apparent. How RNA achieves its large number of different functions with a limited assortment of four differentbuildingblocksisstillaquestionofgreatinterest,andtheanswerliesin decipheringtheRNAstructuresatitsdifferentlevelsofcomplexity.Moredetailed knowledgeaboutthestructuralandfunctionalpropertiesofribonucleicacids,and how they are functioning in the cells, is still required before methods can be developed to use these regulators in solving the problems in molecular medicine. In this book, up-to-date studies are presented, which follow exactly this goal: to v vi Preface understandthestructuresandfunctionsofRNAmoleculesandtousethisinforma- tionforapplicationsincellularbiologyandmolecularmedicine. Over25yearsago,thecentraldogmaofmolecularbiologywasexpandedwith the discovery that in addition to proteins, ribonucleic acids can also exhibit enzy- maticactivities.TheseRNAenzymes(ribozymes)spurredintensestudiesintothe structural basis of RNA catalysis. All naturally occurring ribozymes catalyze phosphodiestertransferorhydrolysiswithexquisitesubstratespecificity. Thus,RNAhasreceivedincreasinginterestasatargetofchemotherapyandas chemotherapeutic agents to be applied in molecular medicine. The demonstration thatsyntheticoligonucleotides couldbeused tointerferewithbiologicalinforma- tiontransferinthe1970softhelastcenturyinducedagreatinteresttoanoveltype of therapy. Oligomeric nucleic acid-based therapeutics can be subdivided into groups according to their target molecule: antisense oligonucleotides (ODN), ribozymes,microRNAsinhibitors,andshortinterferingRNAs.Theseoligonucleotides interactbyWatson–Crickbasepairingwithcellulartranscriptsleadingtotheirdegra- dation or functional inhibition. First antisense therapies have reached the patients. However,arequirementfortheeffectiveapplicationofantisensetherapyisbasedon threefundamentalissues,andtheyarestability,site-specificdelivery,andnooff-target effects.Thisis,ofcourse,alsotruefortheemploymentoftheotherRNAmolecules, such as siRNAs, microRNAs, or different ribozymes. To overcome the stability problems of RNA molecules in the human serum and in the cells, efforts have been directed tochemically modify these ribonucleic acidsin such a way thatthey would becomeresistanttocellularribonucleases.Butwiththesemodificationsonemayalso increasetheunwantedsideeffects,sothattheproblemsofstabilityhavesofarnotbeen optimally solved. Very promising approaches with these goals in mind are also presentedinthisbook. Inthecellsoligonucleotidesareknowntomodulategeneexpressionbybindingto proteins as aptamers, and not only that, in addition, the physiological binding to transcription factors to reduce their capacity to mediate gene transcription has also beenobserved.Veryinterestingandpromisingarealsoantisensemoleculesthatrecruit RNaseHorRISCfactorstomediateRNAhydrolysis.RNAinterference,forexample, isbestknownforitsvariousrolesinposttranscriptionalgenesilencinginthecytoplasm. Inthisvolumethereviewersdiscussthegeneralaspectsofstructureandfunction of ribonucleic acids as indicated above. Very interesting are the results reported, becausetheyshowhownewandverypromisingRNAregulatorscanbedeveloped forthenextgenerationoftherapeuticagentsdirectedatvarioustypesofdiseases. Inthebook,wecollectedchaptersongeneralaspectsofRNA,itsstability,and chemical modification. Several reviews highlight recent progress in development and application of antisense technologies for RNA silencing. The therapeutic potential of ribozymes and DNAzymes is also extensively discussed. A current knowledge on microRNA pathways in human diseases is covered in several chapters and will help to round up the current knowledge of RNA technologies andasthesetechnologiesmaybeappliedinthefieldoffuturemolecularmedicine. Berlin,Germany VolkerA.Erdmann Poznan´,Poland JanBarciszewski Contents RNAissance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 JuergenBrosius NucleicAcidsasTherapeutics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 SaraswatPushpendra,PareekArvind,andBhandariAnil ThioEffectsasaToolforMechanisticStudiesoftheCleavage ofRNAPhosphodiesterBonds:TheChemicalBasis. . . . . . . . . . . . . . 47 MikkoOra,TuomasL€onnberg,andHarriL€onnberg Off-TargetEffectsandSafetyAspectsofPhosphorothioate Oligonucleotides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 MartinaStessl,ChristianR.Noe,andJohannesWinkler OligonucleotideConjugates:Rationale,Synthesis, andApplications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 YashveerSingh,PierreMurat,NicolasSpinelli,andEricDefrancq CRISPR:ABacterialImmunitySystemBasedonSmallRNAs. . . . . . 121 € RolfWagnerandUmitPul AntisenseTechnology:FromUniqueLaboratoryTooltoNovel AnticancerTreatments. . . . . . . .. . . . . . . . . . .. . . . . . . . . . .. . . . . . . 145 ChristineDiCresce,ColinWay,MateuszRytelewski,SamanMalekiVareki, SuprithaNilam,MarkD.Vincent,JamesKoropatnick,andPeterJ.Ferguson Antisense-MediatedReductionofEukaryoticNoncodingRNAs. . . . . 191 Xue-haiLiang,TimothyA.Vickers,andStanleyT.Crooke AntisenseOligonucleotidesintheTreatmentofMalignantGliomas. . 215 GerardoCaruso,MariellaCaffo,GiuseppeRaudino,FedericaRaudino, MarioVenza,andFrancescoTomasello vii viii Contents NaturalAntisenseTranscriptsMediateRegulation ofGeneExpression.. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . . .. . . .. . 247 MarcoMagistriandMohammadAliFaghihi ActivationandDeactivationofAntisenseandRNAInterference FunctionwithLight. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275 JeaneM.GovanandAlexanderDeiters RibozymesasMolecularBiologyReagents. . . . . . . . . . . . . . . . . . . . . . 293 SanchitaBhadra,ArtiPothukuchy,andAndrewEllington RNATechnologiesforMitochondrialGenetics. . . . . . . . . . . . . . . . . . 313 Andre´ Dietrich,KatarzynaRolle,MartaGabryelska,ElizaWyszko, RomainVal,MaciejSzymanski,ClarisseValentin,AnneCosset, andJanBarciszewski RNA-BasedTherapiesforInheritedMetabolicDiseases. . . . . . . . . . . 357 Bele´nPe´rez,MagdalenaUgarte,andLourdesR.Desviat RNA-CleavingDNAEnzymesandTheirPotentialTherapeutic ApplicationsasAntibacterialandAntiviralAgents. . . . . . . . . . . . . . . 371 P.I.PradeepkumarandClaudiaH€obartner HammerheadRibozymesAgainstVirusandViroidRNAs.. . . . . .. . . 411 AlbertoCarbonell,RicardoFlores,andSelmaGago SuppressionofHepatitisCViralGenomeReplication withRNA-CleavingDeoxyribozyme. . . . . . . . . . . . . . . . . . . . . . . . . . . 429 Dal-HeeMinandDong-EunKim DesignofSyntheticshRNAsforTargetingHepatitisC: ANewApproachtoAntiviralTherapeutics. . . . . . . . . . . . . . . . . . . . . 453 BrianH.JohnstonandQingGe TheDiverseActiveSitesinSplicing,Debranching,andMicroRNA ProcessingAroundRNAPhosphodiesterBonds. . . . . . . . . . . . . . . . . . 475 SouravKumarDey,EduardoParedes,MollyEvans,andSubhaR.Das MicroRNAsandTheirAntagonistsasNovelTherapeutics. . . . . . . . . 503 JeppeVinther,JakobLewinRukov,andNoamShomron microRNAsinHumanDiseasesandViralInfections. . . . . . . . . . . . . . 525 AlessandraMescalchinandTobiasRestle DysregulationofMicroRNAExpressionandHumanDiseases?. . . . . . 553 To-HaThai NoncodingRNAs:IdentificationofCancer-Associated MicroRNAs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573 MullerFabbriandGeorgeA.Calin Contents ix TargetingNon-codingRNAsforCancerTherapy. . . . . . . . . . . . . . . . 589 SatyaK.KotaandSavithriBalasubramanian MicroRNAPathwaysinDrosophila. . . . . . . . . . . . . . . . . . . . . . . . . . . 611 GeetanjaliChawlaandNicholasS.Sokol Viroids:TheSmallestKnownInfectiousAgentsCause AccumulationofViroid-SpecificSmallRNAs. . . . . . . . . . . . . . . . . . . 629 JaroslavMatousˇek,DetlevRiesner,andGerhardSteger Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645
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