Base pair - Wikipedia

Mb (= Mbp) = mega base pairs = 1,000,000 bp; Gb = giga base pairs = 1,000,000,000 bp. For single-stranded DNA/RNA, units of nucleotides are used—abbreviated nt ... Basepair FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Unitconsistingoftwonucleobasesboundtoeachotherbyhydrogenbonds Depictionoftheadenine–thymineWatson–Crickbasepair Abasepair(bp)isafundamentalunitofdouble-strandednucleicacidsconsistingoftwonucleobasesboundtoeachotherbyhydrogenbonds.TheyformthebuildingblocksoftheDNAdoublehelixandcontributetothefoldedstructureofbothDNAandRNA.Dictatedbyspecifichydrogenbondingpatterns,"Watson–Crick"(or"Watson–Crick–Franklin")basepairs(guanine–cytosineandadenine–thymine)[1]allowtheDNAhelixtomaintainaregularhelicalstructurethatissubtlydependentonitsnucleotidesequence.[2]Thecomplementarynatureofthisbased-pairedstructureprovidesaredundantcopyofthegeneticinformationencodedwithineachstrandofDNA.TheregularstructureanddataredundancyprovidedbytheDNAdoublehelixmakeDNAwellsuitedtothestorageofgeneticinformation,whilebase-pairingbetweenDNAandincomingnucleotidesprovidesthemechanismthroughwhichDNApolymerasereplicatesDNAandRNApolymerasetranscribesDNAintoRNA.ManyDNA-bindingproteinscanrecognizespecificbase-pairingpatternsthatidentifyparticularregulatoryregionsofgenes. Intramolecularbasepairscanoccurwithinsingle-strandednucleicacids.ThisisparticularlyimportantinRNAmolecules(e.g.,transferRNA),whereWatson–Crickbasepairs(guanine–cytosineandadenine–uracil)permittheformationofshortdouble-strandedhelices,andawidevarietyofnon–Watson–Crickinteractions(e.g.,G–UorA–A)allowRNAstofoldintoavastrangeofspecificthree-dimensionalstructures.Inaddition,base-pairingbetweentransferRNA(tRNA)andmessengerRNA(mRNA)formsthebasisforthemolecularrecognitioneventsthatresultinthenucleotidesequenceofmRNAbecomingtranslatedintotheaminoacidsequenceofproteinsviathegeneticcode. Thesizeofanindividualgeneoranorganism'sentiregenomeisoftenmeasuredinbasepairsbecauseDNAisusuallydouble-stranded.Hence,thenumberoftotalbasepairsisequaltothenumberofnucleotidesinoneofthestrands(withtheexceptionofnon-codingsingle-strandedregionsoftelomeres).Thehaploidhumangenome(23chromosomes)isestimatedtobeabout3.2billionbaseslongandtocontain20,000–25,000distinctprotein-codinggenes.[3][4][5]Akilobase(kb)isaunitofmeasurementinmolecularbiologyequalto1000basepairsofDNAorRNA.[6]ThetotalnumberofDNAbasepairsonEarthisestimatedat5.0×1037withaweightof50billiontonnes.[7]Incomparison,thetotalmassofthebiospherehasbeenestimatedtobeasmuchas4 TtC(trilliontonsofcarbon).[8] Contents 1Hydrogenbondingandstability 1.1Examples 2Baseanalogsandintercalators 3Unnaturalbasepair(UBP) 4Non-canonicalbasepairing 5Lengthmeasurements 6Seealso 7References 8Furtherreading 9Externallinks Hydrogenbondingandstability[edit] Top,aG.Cbasepairwiththreehydrogenbonds.Bottom,anA.Tbasepairwithtwohydrogenbonds.Non-covalenthydrogenbondsbetweenthebasesareshownasdashedlines.Thewigglylinesstandfortheconnectiontothepentosesugarandpointinthedirectionoftheminorgroove. Hydrogenbondingisthechemicalinteractionthatunderliesthebase-pairingrulesdescribedabove.Appropriategeometricalcorrespondenceofhydrogenbonddonorsandacceptorsallowsonlythe"right"pairstoformstably.DNAwithhighGC-contentismorestablethanDNAwithlowGC-content.But,contrarytopopularbelief,thehydrogenbondsdonotstabilizetheDNAsignificantly;stabilizationismainlyduetostackinginteractions.[9] Thebiggernucleobases,adenineandguanine,aremembersofaclassofdouble-ringedchemicalstructurescalledpurines;thesmallernucleobases,cytosineandthymine(anduracil),aremembersofaclassofsingle-ringedchemicalstructurescalledpyrimidines.Purinesarecomplementaryonlywithpyrimidines:pyrimidine-pyrimidinepairingsareenergeticallyunfavorablebecausethemoleculesaretoofarapartforhydrogenbondingtobeestablished;purine-purinepairingsareenergeticallyunfavorablebecausethemoleculesaretooclose,leadingtooverlaprepulsion.Purine-pyrimidinebase-pairingofATorGCorUA(inRNA)resultsinproperduplexstructure.Theonlyotherpurine-pyrimidinepairingswouldbeACandGTandUG(inRNA);thesepairingsaremismatchesbecausethepatternsofhydrogendonorsandacceptorsdonotcorrespond.TheGUpairing,withtwohydrogenbonds,doesoccurfairlyofteninRNA(seewobblebasepair). PairedDNAandRNAmoleculesarecomparativelystableatroomtemperature,butthetwonucleotidestrandswillseparateaboveameltingpointthatisdeterminedbythelengthofthemolecules,theextentofmispairing(ifany),andtheGCcontent.HigherGCcontentresultsinhighermeltingtemperatures;itis,therefore,unsurprisingthatthegenomesofextremophileorganismssuchasThermusthermophilusareparticularlyGC-rich.Ontheconverse,regionsofagenomethatneedtoseparatefrequently—forexample,thepromoterregionsforoften-transcribedgenes—arecomparativelyGC-poor(forexample,seeTATAbox).GCcontentandmeltingtemperaturemustalsobetakenintoaccountwhendesigningprimersforPCRreactions. Examples[edit] ThefollowingDNAsequencesillustratepairdouble-strandedpatterns.Byconvention,thetopstrandiswrittenfromthe5′-endtothe3′-end;thus,thebottomstrandiswritten3′to5′. Abase-pairedDNAsequence: ATCGATTGAGCTCTAGCG TAGCTAACTCGAGATCGC ThecorrespondingRNAsequence,inwhichuracilissubstitutedforthymineintheRNAstrand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC Baseanalogsandintercalators[edit] Mainarticle:Nucleicacidanalogue Chemicalanalogsofnucleotidescantaketheplaceofpropernucleotidesandestablishnon-canonicalbase-pairing,leadingtoerrors(mostlypointmutations)inDNAreplicationandDNAtranscription.Thisisduetotheirisostericchemistry.Onecommonmutagenicbaseanalogis5-bromouracil,whichresemblesthyminebutcanbase-pairtoguanineinitsenolform. Otherchemicals,knownasDNAintercalators,fitintothegapbetweenadjacentbasesonasinglestrandandinduceframeshiftmutationsby"masquerading"asabase,causingtheDNAreplicationmachinerytoskiporinsertadditionalnucleotidesattheintercalatedsite.Mostintercalatorsarelargepolyaromaticcompoundsandareknownorsuspectedcarcinogens.Examplesincludeethidiumbromideandacridine. Unnaturalbasepair(UBP)[edit] Seealso:Artificialgenesynthesis,Expandedgeneticcode,Nucleicacidanalogue,andSyntheticgenomics Anunnaturalbasepair(UBP)isadesignedsubunit(ornucleobase)ofDNAwhichiscreatedinalaboratoryanddoesnotoccurinnature.DNAsequenceshavebeendescribedwhichusenewlycreatednucleobasestoformathirdbasepair,inadditiontothetwobasepairsfoundinnature,A-T(adenine–thymine)andG-C(guanine–cytosine).AfewresearchgroupshavebeensearchingforathirdbasepairforDNA,includingteamsledbyStevenA.Benner,PhilippeMarliere,FloydE.RomesbergandIchiroHirao.[10]Somenewbasepairsbasedonalternativehydrogenbonding,hydrophobicinteractionsandmetalcoordinationhavebeenreported.[11][12][13][14] In1989StevenBenner(thenworkingattheSwissFederalInstituteofTechnologyinZurich)andhisteamledwithmodifiedformsofcytosineandguanineintoDNAmoleculesinvitro.[15]Thenucleotides,whichencodedRNAandproteins,weresuccessfullyreplicatedinvitro.Sincethen,Benner'steamhasbeentryingtoengineercellsthatcanmakeforeignbasesfromscratch,obviatingtheneedforafeedstock.[16] In2002,IchiroHirao'sgroupinJapandevelopedanunnaturalbasepairbetween2-amino-8-(2-thienyl)purine(s)andpyridine-2-one(y)thatfunctionsintranscriptionandtranslation,forthesite-specificincorporationofnon-standardaminoacidsintoproteins.[17]In2006,theycreated7-(2-thienyl)imidazo[4,5-b]pyridine(Ds)andpyrrole-2-carbaldehyde(Pa)asathirdbasepairforreplicationandtranscription.[18]Afterward,Dsand4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole(Px)wasdiscoveredasahighfidelitypairinPCRamplification.[19][20]In2013,theyappliedtheDs-PxpairtoDNAaptamergenerationbyinvitroselection(SELEX)anddemonstratedthegeneticalphabetexpansionsignificantlyaugmentDNAaptameraffinitiestotargetproteins.[21] In2012,agroupofAmericanscientistsledbyFloydRomesberg,achemicalbiologistattheScrippsResearchInstituteinSanDiego,California,publishedthathisteamdesignedanunnaturalbasepair(UBP).[13]ThetwonewartificialnucleotidesorUnnaturalBasePair(UBP)werenamedd5SICSanddNaM.Moretechnically,theseartificialnucleotidesbearinghydrophobicnucleobases,featuretwofusedaromaticringsthatforma(d5SICS–dNaM)complexorbasepairinDNA.[16][22]Histeamdesignedavarietyofinvitroor"testtube"templatescontainingtheunnaturalbasepairandtheyconfirmedthatitwasefficientlyreplicatedwithhighfidelityinvirtuallyallsequencecontextsusingthemodernstandardinvitrotechniques,namelyPCRamplificationofDNAandPCR-basedapplications.[13]TheirresultsshowthatforPCRandPCR-basedapplications,thed5SICS–dNaMunnaturalbasepairisfunctionallyequivalenttoanaturalbasepair,andwhencombinedwiththeothertwonaturalbasepairsusedbyallorganisms,A–TandG–C,theyprovideafullyfunctionalandexpandedsix-letter"geneticalphabet".[22] In2014thesameteamfromtheScrippsResearchInstitutereportedthattheysynthesizedastretchofcircularDNAknownasaplasmidcontainingnaturalT-AandC-Gbasepairsalongwiththebest-performingUBPRomesberg'slaboratoryhaddesignedandinserteditintocellsofthecommonbacteriumE.colithatsuccessfullyreplicatedtheunnaturalbasepairsthroughmultiplegenerations.[10]ThetransfectiondidnothamperthegrowthoftheE.colicellsandshowednosignoflosingitsunnaturalbasepairstoitsnaturalDNArepairmechanisms.Thisisthefirstknownexampleofalivingorganismpassingalonganexpandedgeneticcodetosubsequentgenerations.[22][23]Romesbergsaidheandhiscolleaguescreated300variantstorefinethedesignofnucleotidesthatwouldbestableenoughandwouldbereplicatedaseasilyasthenaturaloneswhenthecellsdivide.Thiswasinpartachievedbytheadditionofasupportivealgalgenethatexpressesanucleotidetriphosphatetransporterwhichefficientlyimportsthetriphosphatesofbothd5SICSTPanddNaMTPintoE.colibacteria.[22]Then,thenaturalbacterialreplicationpathwaysusethemtoaccuratelyreplicateaplasmidcontainingd5SICS–dNaM.Otherresearchersweresurprisedthatthebacteriareplicatedthesehuman-madeDNAsubunits.[24] ThesuccessfulincorporationofathirdbasepairisasignificantbreakthroughtowardthegoalofgreatlyexpandingthenumberofaminoacidswhichcanbeencodedbyDNA,fromtheexisting20aminoacidstoatheoreticallypossible172,therebyexpandingthepotentialforlivingorganismstoproducenovelproteins.[10]TheartificialstringsofDNAdonotencodeforanythingyet,butscientistsspeculatetheycouldbedesignedtomanufacturenewproteinswhichcouldhaveindustrialorpharmaceuticaluses.[25]ExpertssaidthesyntheticDNAincorporatingtheunnaturalbasepairraisesthepossibilityoflifeformsbasedonadifferentDNAcode.[24][25] Non-canonicalbasepairing[edit] Mainarticle:Non-canonicalbasepairing WobblebasepairsComparisonofHoogsteentoWatson–Crickbasepairs.[26] Inadditiontothecanonicalpairing,someconditionscanalsofavourbase-pairingwithalternativebaseorientation,andnumberandgeometryofhydrogenbonds.Thesepairingsareaccompaniedbyalterationstothelocalbackboneshape. ThemostcommonoftheseisthewobblebasepairingthatoccursbetweentRNAsandmRNAsatthethirdbasepositionofmanycodonsduringtranscription[27]andduringthechargingoftRNAsbysometRNAsynthetases.[28]TheyhavealsobeenobservedinthesecondarystructuresofsomeRNAsequences.[29] Additionally,Hoogsteenbasepairing(typicallywrittenasA•U/TandG•C)canexistinsomeDNAsequences(e.g.CAandTAdinucleotides)indynamicequilibriumwithstandardWatson–Crickpairing.[26]Theyhavealsobeenobservedinsomeprotein–DNAcomplexes.[30] Inadditiontothesealternativebasepairings,awiderangeofbase-basehydrogenbondingisobservedinRNAsecondaryandtertiarystructure.[31]Thesebondsareoftennecessaryfortheprecise,complexshapeofanRNA,aswellasitsbindingtointeractionpartners.[31] Lengthmeasurements[edit] ThefollowingabbreviationsarecommonlyusedtodescribethelengthofaD/RNAmolecule: bp=basepair(s)—onebpcorrespondstoapproximately3.4 Å(340 pm)[32]oflengthalongthestrand,andtoroughly618or643daltonsforDNAandRNArespectively. kb(=kbp)=kilobasepairs=1,000bp Mb(=Mbp)=megabasepairs=1,000,000bp Gb=gigabasepairs=1,000,000,000bp. Forsingle-strandedDNA/RNA,unitsofnucleotidesareused—abbreviatednt(orknt,Mnt,Gnt)—astheyarenotpaired. Todistinguishbetweenunitsofcomputerstorageandbases,kbp,Mbp,Gbp,etc.maybeusedforbasepairs. Thecentimorganisalsooftenusedtoimplydistancealongachromosome,butthenumberofbasepairsitcorrespondstovarieswidely.Inthehumangenome,thecentimorganisabout1millionbasepairs.[33][34] Seealso[edit] ListofY-DNAsingle-nucleotidepolymorphisms Non-canonicalbasepairing Chargaff'srules References[edit] ^Spencer,M.(10January1959)."Thestereochemistryofdeoxyribonucleicacid.II.Hydrogen-bondedpairsofbases".ActaCrystallographica.12(1):66–71.doi:10.1107/S0365110X59000160.ISSN 0365-110X. ^ZhurkinVB,TolstorukovMY,XuF,ColasantiAV,OlsonWK(2005).Sequence-DependentVariabilityofB-DNA.DNAConformationandTranscription.pp. 18–34.doi:10.1007/0-387-29148-2_2.ISBN 978-0-387-25579-8. ^MoranLA(2011-03-24)."Thetotalsizeofthehumangenomeisverylikelytobe~3,200Mb".Sandwalk.blogspot.com.Retrieved2012-07-16. ^"Thefinishedlengthofthehumangenomeis2.86Gb".Strategicgenomics.com.2006-06-12.Retrieved2012-07-16. ^InternationalHumanGenomeSequencingConsortium(October2004)."Finishingtheeuchromaticsequenceofthehumangenome".Nature.431(7011):931–45.Bibcode:2004Natur.431..931H.doi:10.1038/nature03001.PMID 15496913. ^CockburnAF,NewkirkMJ,FirtelRA(December1976)."OrganizationoftheribosomalRNAgenesofDictyosteliumdiscoideum:mappingofthenontranscribedspacerregions".Cell.9(4Pt1):605–13.doi:10.1016/0092-8674(76)90043-X.PMID 1034500.S2CID 31624366. ^NuwerR(18July2015)."CountingAlltheDNAonEarth".TheNewYorkTimes.NewYork.ISSN 0362-4331.Retrieved2015-07-18. ^"TheBiosphere:DiversityofLife".AspenGlobalChangeInstitute.Basalt,CO.Retrieved2015-07-19. ^YakovchukP,ProtozanovaE,Frank-KamenetskiiMD(2006-01-30)."Base-stackingandbase-pairingcontributionsintothermalstabilityoftheDNAdoublehelix".NucleicAcidsResearch.34(2):564–74.doi:10.1093/nar/gkj454.PMC 1360284.PMID 16449200. ^abcFikesBJ(May8,2014)."Lifeengineeredwithexpandedgeneticcode".SanDiegoUnionTribune.Archivedfromtheoriginalon9May2014.Retrieved8May2014. 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^Takezawa,Yusuke;Müller,Jens;Shionoya,Mitsuhiko(2017-05-05)."ArtificialDNABasePairingMediatedbyDiverseMetalIons".ChemistryLetters.46(5):622–633.doi:10.1246/cl.160985.ISSN 0366-7022. ^SwitzerC,MoroneySE,BennerSA(1989)."EnzymaticincorporationofanewbasepairintoDNAandRNA".J.Am.Chem.Soc.111(21):8322–8323.doi:10.1021/ja00203a067. ^abCallawayE(May7,2014)."ScientistsCreateFirstLivingOrganismWith'Artificial'DNA".NatureNews.HuffingtonPost.Retrieved8May2014. ^HiraoI,OhtsukiT,FujiwaraT,MitsuiT,YokogawaT,OkuniT,NakayamaH,TakioK,YabukiT,KigawaT,KodamaK,YokogawaT,NishikawaK,YokoyamaS(February2002)."Anunnaturalbasepairforincorporatingaminoacidanalogsintoproteins".NatureBiotechnology.20(2):177–82.doi:10.1038/nbt0202-177.PMID 11821864.S2CID 22055476. ^HiraoI,KimotoM,MitsuiT,FujiwaraT,KawaiR,SatoA,HaradaY,YokoyamaS(September2006)."Anunnaturalhydrophobicbasepairsystem:site-specificincorporationofnucleotideanalogsintoDNAandRNA".NatureMethods.3(9):729–35.doi:10.1038/nmeth915.PMID 16929319.S2CID 6494156. ^Kimoto,M.etal.(2009)AnunnaturalbasepairsystemforefficientPCRamplificationandfunctionalizationofDNAmolecules.NucleicacidsRes.37,e14 ^YamashigeR,KimotoM,TakezawaY,SatoA,MitsuiT,YokoyamaS,HiraoI(March2012)."HighlyspecificunnaturalbasepairsystemsasathirdbasepairforPCRamplification".NucleicAcidsResearch.40(6):2793–806.doi:10.1093/nar/gkr1068.PMC 3315302.PMID 22121213. ^KimotoM,YamashigeR,MatsunagaK,YokoyamaS,HiraoI(May2013)."Generationofhigh-affinityDNAaptamersusinganexpandedgeneticalphabet".NatureBiotechnology.31(5):453–7.doi:10.1038/nbt.2556.PMID 23563318.S2CID 23329867. ^abcdMalyshevDA,DhamiK,LavergneT,ChenT,DaiN,FosterJM,CorrêaIR,RomesbergFE(May2014)."Asemi-syntheticorganismwithanexpandedgeneticalphabet".Nature.509(7500):385–8.Bibcode:2014Natur.509..385M.doi:10.1038/nature13314.PMC 4058825.PMID 24805238. ^SampleI(May7,2014)."FirstlifeformstopassonartificialDNAengineeredbyUSscientists".TheGuardian.Retrieved8May2014. ^ab"ScientistscreatefirstlivingorganismcontainingartificialDNA".TheWallStreetJournal.FoxNews.May8,2014.Retrieved8May2014. ^abPollackA(May7,2014)."ScientistsAddLetterstoDNA'sAlphabet,RaisingHopeandFear".NewYorkTimes.Retrieved8May2014. ^abEvgeniaN.Nikolova;EunaeKim;AbigailA.Wise;PatrickJ.O'Brien;IoanAndricioaei;HashimM.Al-Hashimi(2011)."TransientHoogsteenbasepairsincanonicalduplexDNA".Nature.470(7335):498–502.Bibcode:2011Natur.470..498N.doi:10.1038/nature09775.PMC 3074620.PMID 21270796. ^Murphy,FrankV;Ramakrishnan,V(2004-11-21)."Structureofapurine-purinewobblebasepairinthedecodingcenteroftheribosome".NatureStructural&MolecularBiology.11(12):1251–1252.doi:10.1038/nsmb866.ISSN 1545-9993.PMID 15558050.S2CID 27022506. ^Vargas-Rodriguez,Oscar;Musier-Forsyth,Karin(June2014)."WobbleputsRNAontarget".Nature.510(7506):480–481.doi:10.1038/nature13502.ISSN 1476-4687.PMID 24919145.S2CID 205239383. ^Garg,Ankur;Heinemann,Udo(2017-11-09)."AnovelformofRNAdoublehelixbasedonG·UandC·A+wobblebasepairing".RNA.24(2):209–218.doi:10.1261/rna.064048.117.ISSN 1355-8382.PMC 5769748.PMID 29122970. ^JunAishima,RossitzaK.Gitti,JoyceE.Noah,HinHarkGan,TamarSchlick,CynthiaWolberger(2002)."AHoogsteenbasepairembeddedinundistortedB‐DNA".NucleicAcidsRes.30(23):5244–5252.doi:10.1093/nar/gkf661.PMC 137974.PMID 12466549.CS1maint:multiplenames:authorslist(link) ^abLeontis,NeoclesB;Westhof,Eric(2003)."AnalysisofRNAmotifs".CurrentOpinioninStructuralBiology.13(3):300–308.doi:10.1016/S0959-440X(03)00076-9.PMID 12831880. ^AlbertsB,JohnsonA,LewisJ,MorganD,RaffM,RobertsK,WalterP(December2014).MolecularBiologyoftheCell(6th ed.).NewYork/Abingdon:GarlandScience,Taylor&FrancisGroup.p. 177.ISBN 978-0-8153-4432-2. ^"NIHORDR–Glossary–C".Rarediseases.info.nih.gov.Retrieved2012-07-16. ^ScottMP,MatsudairaP,LodishH,DarnellJ,ZipurskyL,KaiserCA,BerkA,KriegerM(2004).MolecularCellBiology(Fifth ed.).SanFrancisco:W.H.Freeman.p. 396.ISBN 978-0-7167-4366-8....inhumans1centimorganonaveragerepresentsadistanceofabout7.5x105basepairs. Furtherreading[edit] WatsonJD,BakerTA,BellSP,GannA,LevineM,LosickR(2004).MolecularBiologyoftheGene(5th ed.).PearsonBenjaminCummings:CSHLPress.(Seeesp.ch.6and9) SigelA,SigelH,SigelRK,eds.(2012).InterplaybetweenMetalIonsandNucleicAcids.MetalIonsinLifeSciences.10.Springer.doi:10.1007/978-94-007-2172-2.ISBN 978-9-4007-2171-5.S2CID 92951134. CleverGH,ShionoyaM(2012)."Chapter10.AlternativeDNABase-PairingthroughMetalCoordination".InterplaybetweenMetalIonsandNucleicAcids.MetalIonsinLifeSciences.10.pp. 269–294.doi:10.1007/978-94-007-2172-2_10.ISBN 978-94-007-2171-5.PMID 22210343. MeggerDA,MeggerN,MuellerJ(2012)."Chapter11.Metal-MediatedBasePairsinNucleicAcidswithPurineandPyrimidine-DerivedNeucleosides".InterplaybetweenMetalIonsandNucleicAcids.MetalIonsinLifeSciences.10.pp. 295–317.doi:10.1007/978-94-007-2172-2_11.ISBN 978-94-007-2171-5.PMID 22210344. Externallinks[edit] WikimediaCommonshasmediarelatedtoBasepairing. 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