Non-Natural Nucleic Acids: Methods and Protocols

312 Pages·2019·8.317 MB·English

by  Nathaniel Shank

Methods in
Molecular Biology 1973
Nathaniel Shank Editor
Non-Natural
Nucleic Acids
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Non-Natural Nucleic Acids
Methods and Protocols
Edited by
Nathaniel Shank
Department of Chemistry and Biochemistry, Georgia Southern University, Savannah, GA, USA
Editor
NathanielShank
DepartmentofChemistryandBiochemistry
GeorgiaSouthernUniversity
Savannah,GA,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9215-7 ISBN978-1-4939-9216-4 (eBook)
https://doi.org/10.1007/978-1-4939-9216-4
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Preface
DNAhasbecomeauniqueprotagonistin therealmofbioorganic chemistrybecauseofits
predicable and defined structure, succinct programmability, and known interactions and
chemistries.Thishasledtonon-naturalDNAmimics,eitherinpartorinwhole,becoming
integral parts ofnanoscaffolds,detectiondevices, andcritical probesin ahost ofbiological
applications.Thisvolumeaimstohighlightthediverseandexcitingumbrellaofnon-natural
nucleic acids. As nature has served to inspire, it is hoped that this volume will serve as a
meanstoguideresearcherstowardaviablemethodwhenexploringtheirowninquiriesand
toserveasaspringboardfor newendeavors.
Savannah,GA,USA NathanielShank
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 SynthesisandEnzymaticCharacterizationofSugar-Modified
NucleosideTriphosphateAnalogs......................................... 1
StellaDiafa,DamienEve´quoz,ChristianJ.Leumann,
andMarcelHollenstein
2 SynthesisofSite-SpecificCrownEtherAdductstoDNA
0
AbasicSites:8-Oxo-7,8-Dihydro-2-Deoxyguanosine
0
and2-Deoxycytidine.................................................... 15
NaAn,AaronM.Fleming,NicoleC.Rosecrans,YiLiao,
andCynthiaJ.Burrows
3 SynthesisofaFluorescentCytidineTNATriphosphateAnalogue............. 27
HuiMeiandJohnChaput
4 SynthesisofBase-ModifieddNTPsThroughCross-Coupling
ReactionsandTheirPolymeraseIncorporationtoDNA ..................... 39
PetraMe´nova´,HanaCahova´,MilanVra´bel,andMichalHocek
0 0 0
5 2-C,4-C-Ethyleneoxy-Bridged2-DeoxyribonucleicAcids
(EoDNAs)withThymineNucleobases:Synthesis,Duplex-Forming
Ability,andEnzymaticStability........................................... 59
TakashiOsawa,SatoshiObika,andYoshiyukiHari
6 SynthesisProtocolsforSimpleUnchargedGlycolCarbamate
NucleicAcids........................................................... 91
TanayaBoseandVaijayantiA.Kumar
7 SynthesisofNucleobase-FunctionalizedMorpholinoMonomers ............. 107
BappadityaNandi,SankhaPattanayak,SibasishPaul,
JayantaKundu,andSurajitSinha
8 SynthesisandApplicationofLKγTPeptideNucleicAcids.................... 131
NathanielShank,KaraM.GeorgeRosenker,EthanA.Englund,
AndrewV.Dix,ElizabethE.Rastede,andDanielH.Appella
9 AminoglycosideFunctionalizationasaToolforTargeting
NucleicAcids........................................................... 147
DerrickWatkins,KrishnagopalMaiti,andDevP.Arya
10 PreparationandPurificationofOligodeoxynucleotideDuplexes
ContainingaSite-Specific,Reduced,ChemicallyStableCovalent
InterstrandCross-LinkBetweenaGuanineResidueandanAbasicSite........ 163
MaryamImaniNejad,XuGuo,KurtHoush,ChristopherNel,
ZhiyuYang,NathanE.Price,YinshengWang,andKentS.Gates
11 Copper-CatalyzedAlkyne-AzideCycloadditionontheSolidPhase
for thePreparationofFullyClick-ModifiedNucleicAcids ................... 177
MalteRosenthal,FranziskaPfeiffer,andGu¨nterMayer
vii
viii Contents
12 LabelingPeptideNucleicAcidswithIndium-111........................... 185
IgorG.Panyutin
13 Site-SpecificLabelingofDNAviaPCRwithanExpanded
GeneticAlphabet ....................................................... 193
MichaelP.Ledbetter,DenisA.Malyshev,andFloydE.Romesberg
14 FlexibleNucleicAcids(FNAs)asInformationalMolecules:
EnzymaticPolymerizationof fNTPsonDNATemplates
andNonenzymaticOligomerizationofRNAonFNATemplates ............. 213
MarylineChemamaandChristopherSwitzer
15 ArtificialNucleosidesasDiagnosticProbestoMeasureTranslesion
DNASynthesis ......................................................... 237
Jung-SukChoiandAnthonyBerdis
16 FRETAssayforLigandsTargetingtheBacterialA-SiteRNA................. 251
RenatusW.SinkeldamandYitzhakTor
17 TheUseofSerinolNucleicAcidsasUltrasensitiveMolecularBeacons......... 261
KeijiMurayama,HiromuKashida,andHiroyukiAsanuma
18 OligonucleotidePrimerswithG8AE-ClampModifications
forRT-qPCRDetectionoftheLow-CopydsRNA.......................... 281
TimofeiS.Zatsepin,AnnaM.Varizhuk,VladimirG.Dedkov,
GermanA.Shipulin,andAndreyV.Aralov
19 DeterminingSteady-StateKineticsofDNAPolymerase
NucleotideIncorporation................................................ 299
HaileyL.GahlonandShanaJ.Sturla
Index ...................................................................... 313
Contributors
NAAN (cid:2) DepartmentofChemistry,UniversityofUtah,SaltLakeCity,UT,USA
DANIELH.APPELLA (cid:2) NationalInstituteofDiabetesandDigestiveandKidneyDiseases,
NationalInstitutesofHealth,Bethesda,MD,USA
ANDREYV.ARALOV (cid:2) Shemyakin-OvchinnikovInstituteofBioorganicChemistry,Russian
AcademyofSciences,Moscow,Russia
DEVP.ARYA (cid:2) LaboratoryofMedicinalChemistry,DepartmentofChemistry,Clemson
University,Clemson,SC,USA
HIROYUKIASANUMA (cid:2) DepartmentofBiomolecularEngineering,GraduateSchoolof
Engineering,NagoyaUniversity,Nagoya,Japan
ANTHONYBERDIS (cid:2) DepartmentofChemistry,ClevelandStateUniversity,Cleveland,OH,
USA
TANAYABOSE (cid:2) CSIR-NationalChemicalLaboratory,Pune,Maharashtra,India
CYNTHIAJ.BURROWS (cid:2) DepartmentofChemistry,UniversityofUtah,SaltLakeCity,UT,
USA
HANACAHOVA´ (cid:2) InstituteofOrganicChemistryandBiochemistry,CzechAcademyof
Sciences,Prague,CzechRepublic
JOHNCHAPUT (cid:2) DepartmentofPharmaceuticalSciences,UniversityofCalifornia,Irvine,
Irvine,CA,USA;DepartmentofChemistry,UniversityofCalifornia,Irvine,Irvine,CA,
USA;DepartmentofMolecularBiologyandBiochemistry,UniversityofCalifornia,Irvine,
Irvine,CA,USA
MARYLINE CHEMAMA (cid:2) DepartmentofChemistry,UniversityofCalifornia,Riverside,
Riverside,CA,USA
JUNG-SUKCHOI (cid:2) DepartmentofChemistry,ClevelandStateUniversity,Cleveland,OH,
USA
VLADIMIRG.DEDKOV (cid:2) CentralResearchInstituteofEpidemiology,Moscow,Russia
STELLA DIAFA (cid:2) DepartmentofChemistryandBiochemistry,UniversityofBern,Bern,
Switzerland
ANDREWV.DIX (cid:2) NationalInstituteofDiabetesandDigestiveandKidneyDiseases,
NationalInstitutesofHealth,Bethesda,MD,USA
ETHANA.ENGLUND (cid:2) ClinicalResearchManagement,Inc,Gaithersburg,MD,USA
DAMIENEVE´QUOZ (cid:2) DepartmentofChemistryandBiochemistry,UniversityofBern,Bern,
Switzerland
AARONM.FLEMING (cid:2) DepartmentofChemistry,UniversityofUtah,SaltLakeCity,UT,
USA
HAILEYL.GAHLON (cid:2) DepartmentofHealthSciencesandTechnology,ETHZurich,Zurich,
Switzerland
KENTS.GATES (cid:2) DepartmentofChemistry,UniversityofMissouri,Columbia,MO,USA;
DepartmentofBiochemistry,UniversityofMissouri,Columbia,MO,USA
KARAM.GEORGEROSENKER (cid:2) NationalInstituteofDiabetesandDigestiveandKidney
Diseases,NationalInstitutesofHealth,Bethesda,MD,USA
XUGUO (cid:2) DepartmentofChemistry,UniversityofMissouri,Columbia,MO,USA
YOSHIYUKIHARI (cid:2) FacultyofPharmaceuticalSciences,TokushimaBunriUniversity,
Yamashiro-cho,Tokushima,Japan
ix
x Contributors
MICHAL HOCEK (cid:2) InstituteofOrganicChemistryandBiochemistry,CzechAcademy
ofSciences,Prague,CzechRepublic
MARCELHOLLENSTEIN (cid:2) DepartmentofStructuralBiologyandChemistry,Laboratory
forBioorganicChemistryofNucleicAcids,CNRSUMR3523,InstitutPasteur,Paris,
France
KURTHOUSH (cid:2) DepartmentofChemistry,UniversityofMissouri,Columbia,MO,USA
HIROMU KASHIDA (cid:2) DepartmentofBiomolecularEngineering,GraduateSchoolof
Engineering,NagoyaUniversity,Nagoya,Japan;PRESTO,JapanScienceandTechnology
Agency,Kawaguchi,Saitama,Japan
VAIJAYANTIA.KUMAR (cid:2) CSIR-NationalChemicalLaboratory,OrganicChemistryDivision,
Pune,Maharashtra,India
JAYANTAKUNDU (cid:2) DepartmentofOrganicChemistry,IndianAssociationfortheCultivation
ofScience,Jadavpur,Kolkata,India
MICHAELP.LEDBETTER (cid:2) DepartmentofChemistry,TheScrippsResearchInstitute,LaJolla,
CA,USA
CHRISTIAN J.LEUMANN (cid:2) DepartmentofChemistryandBiochemistry,UniversityofBern,
Bern,Switzerland
YILIAO (cid:2) DepartmentofChemistry,UniversityofUtah,SaltLakeCity,UT,USA
KRISHNAGOPALMAITI (cid:2) LaboratoryofMedicinalChemistry,DepartmentofChemistry,
ClemsonUniversity,Clemson,SC,USA
DENIS A.MALYSHEV (cid:2) DepartmentofChemistry,TheScrippsResearchInstitute,LaJolla,
CA,USA
GU¨NTERMAYER (cid:2) ChemicalBiology,LifeandMedicalSciencesInstitute(LIMES),University
ofBonn,Bonn,Germany
HUIMEI (cid:2) DepartmentofChemistry,StanfordUniversity,Stanford,CA,USA
PETRA ME´NOVA´ (cid:2) InstituteofOrganicChemistryandBiochemistry,CzechAcademyof
Sciences,Prague,CzechRepublic
KEIJIMURAYAMA (cid:2) DepartmentofBiomolecularEngineering,GraduateSchoolof
Engineering,NagoyaUniversity,Nagoya,Japan
BAPPADITYANANDI (cid:2) DepartmentofOrganicChemistry,IndianAssociationfor the
CultivationofScience,Jadavpur,Kolkata,India
MARYAMIMANINEJAD (cid:2) DepartmentofChemistry,UniversityofMissouri,Columbia,MO,
USA
CHRISTOPHERNEL (cid:2) DepartmentofChemistry,UniversityofMissouri,Columbia,MO,USA
SATOSHIOBIKA (cid:2) GraduateSchoolofPharmaceuticalSciences,OsakaUniversity,Osaka,
Japan
TAKASHIOSAWA (cid:2) FacultyofPharmaceuticalSciences,TokushimaBunriUniversity,
Yamashiro-cho,Tokushima,Japan
IGORG.PANYUTIN (cid:2) DepartmentofRadiologyandImagingSciences,ClinicalCenter,
NationalInstitutesofHealth,Bethesda,MD,USA
SANKHAPATTANAYAK (cid:2) DepartmentofOrganicChemistry,IndianAssociationfor the
CultivationofScience,Jadavpur,Kolkata,India
SIBASISHPAUL (cid:2) DepartmentofOrganicChemistry,IndianAssociationfor theCultivation
ofScience,Jadavpur,Kolkata,India
FRANZISKAPFEIFFER (cid:2) ChemicalBiology,LifeandMedicalSciencesInstitute(LIMES),
UniversityofBonn,Bonn,Germany
NATHANE.PRICE (cid:2) DepartmentofChemistry,UniversityofCaliforniaRiverside,Riverside,
CA
Contributors xi
ELIZABETHE.RASTEDE (cid:2) NationalInstituteofDiabetesandDigestiveandKidneyDiseases,
NationalInstitutesofHealth,Bethesda,MD,USA
FLOYD E.ROMESBERG (cid:2) DepartmentofChemistry,TheScrippsResearchInstitute,LaJolla,
CA,USA
NICOLEC.ROSECRANS (cid:2) DepartmentofChemistry,UniversityofUtah,SaltLakeCity,UT,
USA
MALTEROSENTHAL (cid:2) ChemicalBiology,LifeandMedicalSciencesInstitute(LIMES),
UniversityofBonn,Bonn,Germany
NATHANIELSHANK (cid:2) DepartmentofChemistryandBiochemistry,GeorgiaSouthern
University,Savannah,GA,USA
GERMANA.SHIPULIN (cid:2) CentralResearchInstituteofEpidemiology,Moscow,Russia;Federal
StateBudgetaryInstitution“Center forStrategicPlanningandManagementof
BiomedicalHealthRisks”oftheMinistryofHealth,Moscow,Russia
SURAJITSINHA (cid:2) DepartmentofOrganicChemistry,IndianAssociationfor theCultivation
ofScience,Jadavpur,Kolkata,India
RENATUS W.SINKELDAM (cid:2) OfficeofTechnologyManagement,WashingtonUniversityinSt.
Louis,St.Louis,MO,USA
SHANAJ.STURLA (cid:2) DepartmentofHealthSciencesandTechnology,ETHZurich,Zurich,
Switzerland
CHRISTOPHERSWITZER (cid:2) DepartmentofChemistry,UniversityofCalifornia,Riverside,
Riverside,CA,USA
YITZHAKTOR (cid:2) DepartmentofChemistryandBiochemistry,UniversityofCalifornia,San
Diego,LaJolla,CA,USA
ANNAM.VARIZHUK (cid:2) ResearchandClinicalCenterforPhysicalChemicalMedicine,Moscow,
Russia;EngelhardtInstituteofMolecularBiology,RussianAcademyofSciences,Moscow,
Russia
MILANVRA´BEL (cid:2) InstituteofOrganicChemistryandBiochemistry,CzechAcademyof
Sciences,Prague,CzechRepublic
YINSHENGWANG (cid:2) DepartmentofChemistry,UniversityofCaliforniaRiverside,Riverside,
CA
DERRICKWATKINS (cid:2) LaboratoryofMedicinalChemistry,DepartmentofChemistry,Clemson
University,Clemson,SC,USA
ZHIYUYANG (cid:2) DepartmentofChemistry,UniversityofMissouri,Columbia,MO,USA
TIMOFEIS.ZATSEPIN (cid:2) SkolkovoInstituteofScienceandTechnology,Skolkovo,Moscow,Russia;
DepartmentofChemistry,LomonosovMoscowStateUniversity,Moscow,Russia