RNA Nanotechnology

452 Pages·2014·27.471 MB·English

by  Bin Wang

RNA
Nanotechnology
TThhiiss ppaaggee iinntteennttiioonnaallllyy lleefftt bbllaannkk
Pan Stanford Series on Renewable Energy — Volume 2
RNA
Nanotechnology
edited by
Bin Wang
editors
Preben Maegaard
Anna Krenz
Wolfgang Palz
The Rise of Modern Wind Energy
Wind Power
for the World
CRC Press
Taylor & Francis Group
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Version Date: 20140307
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January10,2014 17:24 PSPBook-9inx6in 00-Bin–Wang–prelims
Contents
Preface xv
1 Introduction 1
BinWang
2 FundamentalAspectsofRNA 5
ChristianZwieb
2.1 Introduction 5
2.2 TheRNAChain 6
2.3 IntotheFold 8
2.3.1 FoldingPrinciples 8
2.3.2 High-ResolutionRNAStructureMilestones 11
2.3.3 PredictingtheRNAStructure 12
2.3.4 CommonlyObservedRNAMotifs 13
2.4 RNALigands 14
2.4.1 RNA-BindingProteins 14
2.4.2 DrugsTargetingRNA 14
2.5 RNADrugs 15
2.6 Outlook 15
3 ComputationalMethodsforRNAStructurePredictionand
Analysis 21
DavidDufour,EmidioCapriotti,and
MarcA.Marti-Renom
3.1 Introduction 22
3.2 RNAStructure 23
3.2.1 RNABasePairs 24
3.2.2 RNABackbone 25
3.2.3 RNAMotifs 27
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vi Contents
3.3 RNAStructuralDatabases 27
3.4 RNASecondaryStructurePrediction 31
3.5 RNATertiaryStructureAnalysisandPrediction 33
3.5.1 RNA3DStructureAnalysis 33
3.5.2 RNA3DStructurePrediction 35
3.5.3 RNA3DStructureAssessment 38
3.6 Perspectives 39
4 ComputationalModelingforRNAStructureDiscoveryand
Characterization 51
BrianJ.ParkerandThomasPreiss
4.1 Introduction 51
4.1.1 RNAStructurePrediction 53
4.1.1.1 Energy-basedfoldingofasingle
sequence 53
4.1.1.2 Comparativegenomicsapproaches
basedoncovariationofmutations
acrossmultiplesequences 56
4.1.1.3 RNAstructure-specificprofileSCFG
modelsformodelcomparisonand
databasesearch 59
4.1.2 RFAM:ADatabaseofProbabilisticModelsof
StructuralRNAFamilies 60
4.1.3 VisualizingtheRNASecondaryStructure 60
4.1.4 ExperimentalDataforComputationally
PredictedRNASecondaryStructure 61
4.1.5 ExamplesofComputationalAnalysisofNatural
RNAMechanisms 63
4.1.5.1 RNAstructuresinautoregulatory
controlofgeneexpression 64
4.1.5.2 RNAswitchcontrollingmiRNAaction
inhumanp27 64
4.1.5.3 Riboswitches 66
4.2 Conclusion 66
5 TraditionalApproachestoRNAStructureAnalysis 73
JacekWower
5.1 X-RayandNMRStudiesofRNAStructures 73
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Contents vii
5.2 EnzymaticFootprinting 76
5.3 ChemicalProbingofRNASecondaryStructure 78
5.4 MappingMetalIon-BindingPockets 81
5.5 RNACross-Linking 82
5.6 Outlook 85
6 RNAStructure:ProbingBiochemicalAnalyses 93
SubashC.B.Gopinath
6.1 Introduction 94
6.2 NucleotideAnalogInterferenceMapping 97
6.3 RNAIn-LineProbing 100
6.4 Selective2(cid:2)-HydroxylAcylationAnalyzedbyPrimer
Extension 103
6.5 Conclusions 105
7 RNAStructuralAnalysisBasedonThermalDenaturation 111
CarlaA.Theimer,NakeshaL.Smith,and
KhadijahOnanuga-Islam
7.1 Introduction 112
7.2 UV-VisibleAbsorptionSpectroscopy 113
7.2.1 TheHyperchromicEffect 113
7.2.2 BasePairContent 114
7.2.3 TheTwo-StateAssumption 117
7.2.4 RNAFoldingStudiesBasedonThermal
Denaturation 118
7.2.5 ExtendingtheInformationContentofThermal
Denaturation:FluorescentBaseAnalog
Labeling 118
7.3 DifferentialScanningCalorimetry 119
7.3.1 CalorimetryMeasurements 119
7.3.2 ApplicationofDSCtoBiochemical
Investigations 122
7.3.3 InstrumentationAdvances 123
7.4 Outlook 124
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viii Contents
8 ProbingtheStructuralBasisofRetroviralRNAFunctionsvia
NMRSpectroscopy 131
BlantonS.Tolbert,CarrieRollins,JeffreyD.Levengood,LeLuo,
andPrashantRajan
8.1 Introduction 131
8.2 MethodsforPreparingSegmentallyLabeledRNA 133
8.3 NMRDetectionofRNAStructuresInvolvedin
RetroviralPackagingMechanisms 136
8.3.1 TheMurineLeukemiaVirus 136
8.3.2 TheHumanImmunodeficiencyVirus-1 140
8.4 MechanisticInsightsintotRNAPrimingofReverse
TranscriptioninHIVMonitoredbyNMRSpectroscopy 144
8.5 Conclusion 147
9 ProbingtheFoldingandStructuralDynamicsinRNAsby
Single-MoleculeApproaches 153
GuangtaoSongandMaumitaMandal
9.1 Introduction 153
9.2 Single-MoleculeApproaches 155
9.2.1 Single-MoleculeForceSpectroscopy 155
9.2.1.1 Atomicforcespectroscopy 156
9.2.1.2 Magnetictweezers 156
9.2.1.3 Opticaltweezers 157
9.2.2 Single-MoleculeFluorescenceSpectroscopy 157
9.2.2.1 Confocalmicroscopy 158
9.2.2.2 TIRFmicroscopy 158
9.2.2.3 smFRET 158
9.2.3 CombinedApproaches 159
9.3 Single-MoleculeStudiesonRNA 159
9.3.1 FoldingofSimpleSecondaryandTertiary
Structures 159
9.3.2 FoldingandStructuralDynamicsofLarge
FunctionalRNAStructures 164
9.3.2.1 Ribozyme 164
9.3.2.2 Riboswitch 166
9.3.2.3 Ribosome 171
9.4 SummaryandProspects 175
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Contents ix
10 ApplicationofSingle-MoleculeFluorescenceinRNABiology 185
PanT.X.LiandLoriGoldner
10.1 Introduction 185
10.1.1 Single-MoleculeApproachtotheRNA
StructureProblem 186
10.1.2 FluorescenceProbesforSingle-Molecule
Studies 187
10.1.3 Single-Molecule-SensitiveMicroscopies 189
10.2 MonitoringtheDynamicsofSingleRNAMolecules
UsingFRET 190
10.2.1 FoldingofaTetraloopReceptor 191
10.2.2 HairpinRibozymes 193
10.2.3 LargeRibozymes 195
10.2.3.1 GroupIintronribozymes 195
10.2.3.2 GroupIIintronribozymes 196
10.2.4 Riboswitches 197
10.3 RNAasPartofaMolecularMachinery 198
10.3.1 CountingRNAMoleculesina
Bacteriophage-PackagingMotor 198
10.3.2 AssemblyandActivityofTelomerase 199
10.3.3 MonitorSplicinginRealTime 200
10.3.4 TranslationbyRibosomes 202
10.4 Conclusion 204
11 RationalDesignofRNANanoparticlesandNanoarrays 213
ArkadiuszChworos
11.1 Introduction:DevelopmentofDNA
Nanotechnologies 213
11.2 RNAModularFunctions 215
11.3 VocabularyofRNAMotifs 216
11.4 RationalDesignoftheFirstRNASelf-Assembly
Units 217
11.5 TheConceptoftheRNA“Lego”Playground 218
11.6 Creatingtecto-RNASquaresUsingRNAJunction
Motifs 221
11.7 FromModelTetramerstoMultidimensional
Assemblies 225
11.8 UsingRNANanoparticlestowardGeneRegulation 227