NUCLEOTIDESANDTHEDOUBLEHELIX

DNA,ordeoxyribonucleicacid,istheheritablematerialfoundinallcells.DNAprovidestheinstructionsto
build,maintain,andregulatecellsandorganismsandispassedonwhencellsdivideandwhenorganisms
reproduce.Inthisunit,themolecularstructureofDNAanditspackagingwithincellswillbeexamined.In
1953,usingdataobtainedbyRosalindFranklin,JamesWatsonandFrancisCrickdeterminedthatDNAexistsin
aformknownasthedoublehelix.AhelixisawindingstructurelikeacorkscrewDNAisknownasadouble
helixbecausetherearetwointertwinedstrandswithineachmoleculeofDNA.

Intheimageabove,acorkscrewisshownontheleft,withthehelicalregionlabeled.Theimageinthecenter
showsthestructureofDNA.Notethattherearetwostrands:oneshowninblue,oneinyellow.Other
examplesofahelixincludeyarn,aphonecord,oraspiralstaircase.
Eachchainofthedoublehelixismadeupofrepeatingunitscallednucleotides.Asinglenucleotideis
composedofthreefunctionalgroups:asugar,atriphosphate,andanitrogenous(nitrogencontaining)base,
asshownbelow.Notethatinthefiguresdrawninthisunit,eachunlabeledvertexofastructurerepresentsa
carbonatom.

ThesugarfoundinDNAisavariantofthefivecarbonsugarcalledribose.Thestructureofriboseisdrawn
below.Eachcarbonofriboseisnumberedasshown.BecausetheOHgrouponthe2carbonismissinginthe
formofribosefoundinDNA,thesugarinDNAiscalled2deoxyribose.

Thesecondprinciplefeatureofanucleotideisthetriphosphategroupattachedtothe5carbonoftheribose
group.Inanaqueousenvironment,likeinsidethecell,thephosphategroupsarenegativelycharged,asdrawn
inthefigureabove.
Afree,unincorporatednucleotideusuallyexistsinatriphosphateformthatis,itcontainsachainofthree
phosphates.InDNA,however,itlosestwoofthesephosphategroups,sothatonlyonephosphateis
incorporatedintoastrandofDNA.WhennucleotidesareincorporatedintoDNA,adjacentnucleotidesare
linkedbyaphosphodiesterbond:acovalentbondisformedbetweenthe5phosphategroupofonenucleotide
andthe3OHgroupofanother(seebelow).Inthismanner,eachstrandofDNAhasabackboneof
phosphatesugarphosphatesugarphosphate.Thebackbonehasa5end(withafreephosphate)anda3end
(withafreeOHgroup).Inthestructurebelow,eachnucleotideisdrawninadifferentcolor,forclarity.

Thethirdprinciplefeatureofanucleotideisthebase,whichisattachedtothe1carbonoftheribose.
AlthougheachnucleotideinDNAcontainsidenticalsugarandphosphategroups,therearefourdifferentbases
andthusfourdifferentnucleotidesthatcanbeincorporatedintoDNA.Thefourbasesareadenine,cytosine,
guainne,andthymine,andtheirstructuresareshownbelow.

Whenthesebasesareincorporatedintonucleotides,thenucleotidesarecalled2deoxyadenosinetriphosphate,
2deoxycytidinetriphosphate,2deoxyguanosinetriphosphate,and2deoxythymidinetriphosphate,respectively.
WeoftenshortenthisnotationtoA,C,G,andT.Notethattwopairsofbaseshavesimilarstructures.AandG
bothhavetwocarbonnitrogenringsandareknownaspurines.Incontrast,CandThaveasinglecarbon
nitrogenringandbelongtoaclassofmoleculescalledpyrimidines.

HydrogenbondinteractionsbetweenthebasesallowtwostrandsofDNAtoformthedoublehelix.These
interactionsarespecific:AbasepairswithT,andCbasepairswithG.Thisoccursviahydrogenbonds,which
areshownwithdottedlinesinthefigureabove.IfDNAwerethoughtofasaspiralstaircase,thebasepairs
wouldbethesteps.Thewidthofeachstepisapproximatelythesamesize,sinceabasepairalways
consistsofonepyrimidineandonepurine.ThestrandsofDNArunantiparallel,orinoppositedirections:the
5endofonestrandispairedwiththe3endoftheother.Thisisillustratedinthefigurebelow.

ThisstructureplacesthenonpolarbasesofDNAinthecenterofthedoublestrandedmolecule,surroundedby
thechargedphosphategroups.Thishastwofunctionalconsequences.First,rememberthatlikechargesrepel
eachother.Thedoublehelixstructure,withnegativelychargedphosphatesontheoutsideedges,allowsthe
phosphatestobeasfarapartaspossible.Second,thenonpolar,unchargedbasesarehiddeninthecenterof
thehelix.Thecellularenvironmentisaqueousandthereforepolar,sosurroundingthenonpolarbaseswith
chargedphosphatesmaximizesthesolubilityofDNAunderphysiologicalconditions.Moreinformationon
polaritycanbefoundinthetutorialonbonding.
Becauseofthespecificityofhydrogenbonding,inthecontextofDNAAalwayspairswithT,andGwithC.
Therefore,ifthesequenceofonestrandofDNAisknown,thesequenceoftheotherstrandcanbedetermined
aswell.Inthisway,ifonestrandofDNAisknowntohavethesequence5ATGGCT3,theotherstrandmust
havethesequence3TACCGA5.(Rememberthatthestrandsrunantiparallel,sothe5endofonestrand
mustbeabletopairwiththe3endoftheother.)Thesestrandsarecalledcomplementary.