Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications

599 Pages·2014·16.77 MB·English

by  Volker A. Erdmann

RNA Technologies
Volker A. Erdmann
Wojciech T. Markiewicz
Jan Barciszewski Editors
Chemical
Biology of
Nucleic Acids
Fundamentals and Clinical Applications
RNA Technologies
For furthervolumes:
http://www.springer.com/series/8619
ThiSisaFMBlankPage
Volker A. Erdmann (cid:129) Wojciech T. Markiewicz (cid:129)
Jan Barciszewski
Editors
Chemical Biology of Nucleic
Acids
Fundamentals and Clinical Applications
Editors
VolkerA.Erdmann WojciechT.Markiewicz
InstituteofChemistry/Biochemistry JanBarciszewski
FreeUniversityBerlin InstituteofBioorganicChemistry
Berlin,Germany PolishAcademyofSciences
Poznan,Poland
ISBN978-3-642-54451-4 ISBN978-3-642-54452-1(eBook)
DOI10.1007/978-3-642-54452-1
SpringerHeidelbergNewYorkDordrechtLondon
LibraryofCongressControlNumber:2014937792
©Springer-VerlagBerlinHeidelberg2014
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Preface
ThisyeartheRNAtechnologiesarecelebratingtwoveryimportantanniversaries.
Thefirstoneisthe60thanniversaryofthefoundingoftheRNATieClubandthe
other one is the 40th anniversary of the successful crystallization and structural
determinationofthephenylalanine-specifictRNAfromyeast.
The 60th anniversary of the RNA Tie Club is indeed a very important date to
remember! The 20 members of this club, among them Sydney Brenner, Erwin
Chargaff,FrancisCrick,MaxDelbru¨ck,PaulDoty,GeorgeGamow,LeslieOrgel,
AlexanderRich,GuntherStent,andJamesWatson,hadrealizedtothesurpriseof
everyone, only 1 year after Watson and Crick had determined the double helical
structureforDNA(WatsonandCrick1953),thatthereseemstobemuchmoreto
RNAmoleculesthananticipated.
Indeed, Watson and Crick had surprised everyone with the statement in their
DNA paper concerning RNA molecules: “It is impossible to build this structure
with a ribose sugar in place of the deoxyribose, as the extra oxygen atom would
maketoocloseavanderWaalscontact”(WatsonandCrick1953).Itwastherefore
notexpectedwhen1yearlatertheRNATieClubwasfoundedwiththegoalto“to
solvetheriddleoftheRNAstructureandtounderstandhowitbuiltproteins”.
ThemembersoftheRNATieClubhadselectedtheguideslogan“Doordie,or
don’t try”. Thus, very intensive RNA structural and functional studies were initi-
ated,inwhichAlexanderRichplayedakeyrole.Indeed,Richcoulddemonstratein
thefollowingyearsthatRNAmayformWatsonandCrickbasepairs,thatanRNA
strand could base pair with a DNA strand and that even triple strand nucleic acid
structures were possible (Rich personal communication; Rich 2009). With the
determinationofthethree-dimensionaltRNAstructure40yearsagobytheresearch
groups from Alexander Rich (Kim et al. 1973) and Aaron Klug (Robertus
etal.1974),theunforeseendiversityofRNAstructuralpotentialsbecameapparent
forthefirsttime,anditcanbesafetoassumethatwearestilllackingthecomplete
knowledgeofallstructuralpossibilitiesoftheRNAmolecules.
Paralleltothestructuralactivities,studieswereinitiatedinwhichthechemistry
of nucleic acids was developed, so that oligonucleotides could be chemically
v
vi Preface
synthesized.Itwastheknowledgeofthechemicalsynthesisofnucleicacidswhich
turnedouttobethekeytounlockthesecretsofthegeneticcode.
ClearlytheseearlyRNAstudiesrequiredthesignificantinvolvementofnucleic
acid chemistry, which later on with the rapid developments of molecular biology
andmoleculargeneticsseemedtobelessandlessimportant.Butnowinthelastfew
yearstherehasbeenauniquerevivaloftheemploymentofnucleicacidchemical
methodsinthenaturalsciences,sothatwearecurrentlyspeakingofthenewfieldof
chemicalbiology.
We,astheeditorsofthisvolumeintheRNATechnologiesSeries,areveryhappy
to present to the reader 29 of the world leading research groups in the area of
chemicalbiology.Youwillseethattheexitingresearchcarriedoutbythesegroups
willintroduceustonewideashowchemistrycanaddnewelementstotheareasof
nucleic acids in biotechnologies, nanotechnologies, and, very importantly, in the
areasofdiagnosticsandtherapyinthefieldofmolecularmedicine.
ThisnewvolumeofRNATechnologiesstartswithacontributiondevotedtothe
newly defined field named pre-biology. The majority of papers address in a new
way the fundamental questions: how the early genetic code was developed, how
stableandpronetoisomerisationRNAsare,andhowstablenucleobasesinRNAs
are.Thesearchforalternativeandmodifiednucleobasesystemshasbothasenseof
basic questions and also applicational aspects in the fields of new approaches in
therapies and technologies. In a similar context one can view the questions
discussed in papers dealing with structural aspects of nucleic acids. The coped
knowledge is very rich, yet it seems that still many possible structural features of
nucleicacidsaretobediscovered.Forexample,thedynamicstructuresofnucleic
acids and their analogs, with their ingenious modifications in the sugar moiety,
whichforexample,determinetheirbiologicalfunctionsinprocessessuchasDNA
replication. But also very interestingly, their extra- and intracellular transport are
the subject of several papers. This includes, for example, the important
G-quadruplex motifs as potential therapeutic targets and still double-stranded
nucleicacidsasimportantmoleculartools.
Thedevelopmentoftechnologiessuitabletomodifythelevelofgeneexpression
is remarkable as well. The possibility of exon skipping by chemically modified
RNAs brings again a new element to RNA functions. These technologies include
editing of therapeutic genes, using modified riboswitches and approaches that are
basedonmodificationofCapregionsofthemRNAs.Notoverlookedshouldbethe
developmentsofnewpowerfulapproachestodetectnucleicacidsandtheapplica-
tions of appropriately modified RNAs by electron paramagnetic resonance (EPR)
spectroscopy. One very interesting contribution, as a representative of these tech-
niques,isalsopresentedinthisbook.
Andfinally,wewouldliketobringthereaders’attentiontonewapproachesto
study structure and interactions of nucleic acids and other biomolecules in an
environment that is offered by ionic liquids. This field widens the range of obser-
vations of the most important biological molecules and might be considered as a
step towards studying their structure and interactions under the conditions of
molecularcrowding,whichisotherwisehardlyaccessiblefordetailedanalysis.
Preface vii
Theorderofthechaptersinthebookcouldperhapsalsobeadifferentone.But
thisismoreapersonalopinion,becausetheareascoveredinthefieldofchemical
biologyaresodiversethatitshouldtemptthereadertojustgothroughthebookand
readthechapterswhichinteresthimatthattimethemost.
In summary, we hope that this new volume of RNA Technologies will be of
interest for chemists, biochemists, and life scientists and that it will not only
stimulatetheirresearchbutalsoourfutureresearch.
Berlin,Germany VolkerA.Erdmann
Poznan,Poland WojciechT.Markiewicz
January,2014 JanBarciszewski
References
KimSH,QuigleyGJ,SuddathFLetal(1973)Three-dimensionalstructureofyeastphenylalanine
transferRNA:foldingofthepolynucleotidechain.Science179:285–288
RichA(2009)TheeraofRNAawakening:structuralbiologyofRNAintheearly.QRevBiophys
42:117–137
Robertus JD, Ladner JE, Finch JT et al (1974) Structure of yeast phenylalanine tRNA at 3 Å
resolution.Nature250:546–551
Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose
nucleicacid.Nature171:737–738
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Contents
RNAasMajorComponentsinChemicalEvolvableSystems. . . . . . . 1
PeterStrazewski
HowtheEarlyGeneticCodeWasEstablished?:Inferencefrom
theAnalysisofExtantAnimalMitochondrialDecodingSystems. . . . 25
KimitsunaWatanabeandShin-ichiYokobori
IsomerizationofRNAPhosphodiesterLinkages. . . . . . . . . . . . . . . . 41
HarriLo¨nnberg
EffectsofIonicLiquidandLiposomesontheStructure,Stability,
andFunctionofNucleicAcids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
NaokiSugimoto
OxidativeDamageonRNANucleobases. . . . . . . . . . . . . . . . . . . . . . 75
PascalA.Ku¨pferandChristianJ.Leumann
UseofFRETtoStudyDynamicsofDNAReplication. . . . . . . . . . . . 95
PhilipNevinandPennyJ.Beuning
Design,Characterization,andApplication
ofImidazopyridopyrimidine:NaphthyridineBase-PairingMotifs
ConsistingofFourHydrogenBonds. . . . . . . . . . . . . . . . . . . . . . . . . 113
NoriakiMinakawaandAkiraMatsuda
CreationofUnnaturalBasePairSystemsTowardNewDNA/RNA
Biotechnologies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
MichikoKimotoandIchiroHirao
FlexibleNucleobaseAnalogues:NovelToolsforExploring
NucleicAcids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
SarahC.ZimmermannandKatherineL.Seley-Radtke
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