Structure of DNA

The present slide describes the DNA Structures and the components of the DNA along with the illustrative structures.

1. Structure of DNA

2. ✓Althoughthenamenucleicacidsuggeststheirlocation
inthenucleiofcells,certainofthemare,however,also
presentinthecytoplasm.
✓Thenucleicacidsarethehereditarydeterminantsof
livingorganisms.
✓Theyarethemacromoleculespresentinmostliving
cellseitherinthefreestateorboundtoproteinsas
nucleoproteins.
✓Liketheproteins,thenucleicacidsarebiopolymersof
highmolecularweightwithmononucleotideastheir
repeatingunits,justasaminoacidsaretherepeating
unitsofproteins.

3. ✓Therearetwokindsofnucleicacids,deoxyribonucleic
acid(DNA)andribonucleicacid(RNA).
✓Bothtypesofnucleicacidsarepresentinallplantsand
animals.
✓DNAisfoundmainlyinthechromatinofthecell
nucleuswhereasmostoftheRNA(90%)ispresentin
thecellcytoplasmandalittle(10%)inthenucleous.
✓ItmaybeaddedthatextranuclearDNAalsoexists;it
occurs,forexample,inmitochondriaandchloroplasts.

4. Hydrolytic products of nucleic acid

5. Components RNA DNA
Acid Phosphoric acidPhosphoric acid
Pentose sugarRibose 2-deoxyribose
Nitrogenousbases
Purines Adenine
Guanine
Adenine
Guanine
Pyrimidines Cytosine
Uracil
Cytosine
Thymine
Components of nucleic acids

6. PhosphoricAcid
✓ThemolecularformulaofphosphoricacidisH
3PO
4.
✓Itcontains3monovalenthydroxylgroupsanda
divalentoxygenatom,alllinkedtothepentavalent
phosphorusatom

7. PentoseSugar
✓Thetwotypesofnucleicacidsaredistinguishedprimarily
onthebasisofthe5-carbonketosugarorpentosewhich
theypossess.
✓OnepossessesD-2-deoxyribose,hencethename
deoxyribosenucleicacidordeoxyribonucleicacid,while
theothercontainsD-ribose,hencethenameribosenucleic
acidorribonucleicacid.

8. ✓Animportantpropertyofthepentosesistheircapacity
toformesterswithphosphoricacid.
✓InthisreactiontheOHgroupsofthepentose,especially
thoseatC3andC5,areinvolvedforminga3′,5′-
phosphodiesterbondbetweenadjacentpentoseresidues.
✓Thisbond,infact,isanintegralpartofthestructureof
nucleicacids.

10. NitrogenousBases
✓Twotypesofnitrogenousbasesarefoundinallnucleic
acids.
✓Thenitrogenousbasesarederivativesofpyrimidineand
purine.
✓Pyrimidinebases–Uracil,ThymineandCytosine
✓Purinebases–Adenineandguanine

11. PyrimidineDerivatives
✓Theseareallderivedfromtheirparentheterocyclic
compoundpyrimidine,whichcontainsasixmembered
ringwithtwo-nitrogenatomsandthreedoublebonds.
✓Ithasameltingpointof22°Candaboilingpointof
123.5°C.

12. Uracil(C
4H
4O
2N
2),foundinRNAonly,MW=112.10
daltons,M.P-338°C.
Thymine(C
5H
6O
2N
2),foundinDNAonly,MW=126.13
daltons,M.P-335°C.
Cytosine(C
5H
4ON
3),foundinbothDNAandRNA,MW=
111.12daltons,M.P–320-325°C

13. PurineDerivatives
✓Theseareallderivedfromtheirparentcompound
purine,whichcontainsasix-memberedpyrimidinering
fusedtothefive-memberedimidazoleringandis
relatedtouricacid.
✓Ithasameltingpointof216°C.

14. Adenine(C
5H
5N
5),foundinbothRNAandDNA,withMW
=135.15daltonsandM.P.360-365°C.
Guanine(C
5H
5ON
5),alsofoundinbothRNAandDNA,
withMW=151.15daltonsandM.P.360°C

15. ✓Thenucleosidesarecompoundsinwhichnitrogenous
bases(purinesandpyrimidines)areconjugatedtothe
pentosesugars(riboseordeoxyribose)byaβ-
glycosidiclinkage.
✓Theβ-glycosidiclinkageinvolvestheC-1′ofsugarand
thehydrogenatomofN-9(inthecaseofpurines)orN-
1(inthecaseofpyrimidines),thuseliminatinga
moleculeofwater.
Nucleosides

16. Nucleosides

18. ✓Nucleotidesarethephosphoricacidestersof
nucleosides.
✓Theseoccureitherinthefreeformorassubunitsin
nucleicacids.
✓Intheribosemoietyofaribonucleoside,
phosphorylationispossibleonlyatthreepositions(C2′,
C3′,C5′)sinceC1′andC4′areinvolvedinthefuranose
ringformation.
✓Inthedeoxyribosecomponentofa2′-
deoxyribonucleoside,onlytwopositions(C3′,C5′)are
availableforphosphorylation,sinceinthissugarC1′
andC4′areinvolvedinthefuranoseringandC2′does
notbearahydroxylgroup.
Nucleotides

19. Nucleotides

20. Deoxyribonucleic Acid
✓Anucleicacidmaybevisualizedasapolymerofa
nucleotidemonomer.
✓Inotherwords,itmaybeconsideredasa
polynucleotide.
✓DNAas....(base-deoxyribose-phosphate)
n
✓RNAas....(base-ribose-phosphate)
n

21. BaseCompositionofDNA-ChargaffRule
✓Thesumofpurines(Pu)isequaltothesumof
pyrimidines(Py),i.e.,Pu/Py=1.Inotherwords,A+G
=T+C
✓Theratioofadeninetothymineisalsoone,i.e.,A/T=
1.
✓Theratioofguaninetocytosineisalsoone,i.e.,G/C=
1.
✓Baseswith6-aminogroupsareequaltobaseswith6-
keto(hydroxyl)groups,i.e.,A+C=G+T.
✓TheratioofA+T/G+C,knownasdissymmetryratio,
variesgreatlyfromonespeciesofDNAtotheother
andischaracteristicofthatspecies.
✓Chargaff’sdatasuggestthatAisalwayspairedwithT
andGisalwayspairedwithC.

22. Primary structure
✓PrimarystructureofDNAreferstothephosphodiester
bondbackbone.
✓Innucleicacidstrands,nucleotidesarelinkedby
phosphodiesterbond.
✓Thebondisformedbetweenthe5’-phosphategroupof
onenucleotideand3—hydroxylgroupofadjacent
nucleotide.
✓Asinglenucleicacidstrandformedbyphosphodiester
bondhastwotermininamely5’endwithphosphategroup
and3’endwithhydroxylgroup.

24. Secondary Structure
✓DoublehelicalDNAmodelwasproposedbyWatson
andCrick.
✓ThismodelisalsocalledasB-form.
✓DNAdoublehelixismadeupoftwoDNAstrands
runninginoppositedirectionsalongacommonaxis.
✓ApairswithTviatwohydrogenbondsandGpairswith
Cviathreehydrogenbonds.
✓DNAwillhave1:1ratioofpurineandpyrimidinebases
(Chargaff’srule).

26. Tertiary structure
✓Supercoiled,DNA,chromosomesandchromatinarethe
threetypesoftertiarystructuresofDNA
✓DNAcanbetwisted,coiledintocompactstructurewhich
resemblesacoiledtelephonewire
✓Supercoilingmayberighthandedorlefthanded.

28. Double Helical Structure of DNA
(Watson-Crick Model)
✓DNAmoleculeconsistsoftwohelicalpolynucleotide
chainswhicharecoiledaround(orwrappedabout)a
commonaxisintheformofaright-handeddoublehelix.
✓Thetwohelicesarewoundinsuchawaysoasto
produce2interchainspacingorgrooves,amajororwide
groove(width12Å,depth8.5Å)andaminorornarrow
groove(width6Å,depth7.5Å).

30. ✓Thephosphateanddeoxyriboseunitsarefoundonthe
peripheryofthehelix,whereasthepurineand
pyrimidinebasesoccurinthecentre.
✓Theplanesofthebasesareperpendiculartothehelix
axis.
✓Theplanesofthesugarsarealmostatrightanglesto
thoseofthebases.

31. ✓Thediameterofthehelixis20Å.
✓Thebasesare3.4Åapartalongthehelixaxis.
✓Therefore,thehelicalstructurerepeatsafter10
residuesoneachchain,i.e.,atintervalsof34Å.
✓Inotherwords,eachturnofthehelixcontains10
nucleotideresidues.

32. ✓Thetwochainsareheldtogetherbyhydrogenbonds
betweenpairsofbases.
✓Adeninealwayspairswiththymineby2hydrogenbonds
andguaninewithcytosinewith3hydrogenbonds.
✓Theindividualhydrogenbondsareweakinnaturebut,as
inthecaseofproteins,alargenumberoftheminvolved
intheDNAmoleculeconferstabilitytoit.
✓ItisnowthoughtthatthestabilityoftheDNAmolecule
isprimarilyaconsequenceofvanderWaalsforces
betweentheplanesofstackedbases.

33. ✓Thesequenceofbasesalongapolynucleotidechainis
notrestrictedinanyway.
✓Theprecisesequenceofbasescarriesthegenetic
information.
✓Asacorollary,theentirestructureofaDNAmolecule
resemblesawindingstaircase,withthesugarand
phosphatemoleculesofthenucleotidesformingthe
railingsandthelinkednitrogenbasepairs(A-TandG-
C)formingthesteps.

34. A-DNA
✓A-DNAappearswhentheDNAfibre(B-DNA)is
dehydrated,i.e.,relativehumidityisreducedfrom92to
75%andNa
+
,K
+
andCs
+
ionsarepresentinthe
medium.Inotherwords,insolution,DNAassumesthe
BformandafterdehydrationitassusmestheAform.
✓ThisisbecausethephosphategroupsintheA-DNA
bindfewerwatermoleculesthanthephosphatesinB-
DNA.

36. C-DNA
✓C-DNAisformedat66%relativehumidityinthe
presenceofLi
+
ions.
✓ThisformofDNAisalsoright-handed,withanaxial
riseof3.32Åperbasepair.
✓Thereare9.33basepairperturnofthehelix;thevalue
ofhelixpitchis,therefore,3.32×9.33Åor30.97Å.
✓TherotationperbasepairinC-DNAis360/9.33or
38.58°.
✓TheC-helixhasadiameterof19Å,smallerthanthat
ofbothB-andA-helix.

38. D-DNA
✓D-DNAisanextremelyrarevariantwithonly8base
pairsperhelicalturn.
✓ThisformofDNAisfoundinsomeDNAmolecules
devoidofguanine.
✓Bycontrast,A-,B-andCformsofDNAarefoundinall
DNAmolecules,irrespectiveoftheirbasesequence.

40. Z-DNA
✓Z-DNAisthemoreradicaldeparturefromB-DNAand
ischaracterizedbyalefthandedhelicalrotation.
✓ItwasdiscoveredbyRich,NordheimandWangin
1984.
✓Theyfoundthatahexanucleotide,CGCGCG,formsa
duplexofantiparallelstrandsheldtogetherbyWatson-
Crickbasepairing,asexpected.
✓Surprisingly,theyfoundthatthisdoublehelixwasleft-
handedandthephosphatesintheDNAbackbonewere
inazigzagmanner;hence,theytermedthisnewform
asZ-DNA.

42. PalindromicDNA
✓It has sequences with twofold symmetry.
✓In order to superimpose one repeat (shaded sequence) on
the other (unshadedsequence), it must be rotated 180°
around the horizontal axis and then again about the
vertical axis, as shown by arrows.

43. Mirrorrepeat
✓Ithasasymmetricsequenceoneachstrand.
Superimposingonerepeatontheotherrequiresonlya
single180ºrotationabouttheverticalaxis.

44. BentDNA
✓SomesequencescausebendsintheDNAhelix.
✓Bendsareproducedwhenever4ormoreadenine
residuesappearsequentiallyinoneofthetwostrands.
✓Sixadeninesinarowproduceabendofabout18°.
✓Bendingmaybeimportantinthebindingofsome
proteinstoDNA.
Hairpin
✓WhenonlyasinglestrandofpalindromicDNA(or
RNA)isinvolved,ahairpinisformed.
Cruciform
✓WhenboththestrandsofadoublehelicalDNAare
involved,acruciformisformed.

46. H-DNA
✓H-DNAisusuallyfoundinpolypyrimidineor
polypurinesegmentsthatcontainwithinthemselvesa
mirrorrepeat.
✓OnesimpleexampleisalongstretchofalternatingT
andCresidues.
✓AstrikingfeatureofH-DNAisthepairingand
interwindingof3strandsofDNAtoformatriplehelix.
✓Triple-helicalDNAisproducedspontaneouslyonly
withinlongsequencescontainingonlypyrimidines(or
purines)inonestrand.
✓TwoofthethreestrandsintheH-DNAtriplehelix
containpyrimidinesandthethirdcontainspurines.