NUCLEICACIDS:DNAANDRNAHLeeYuJsuicoJunsay

DepartmentofChemistry

SchoolofScienceandEngineering

AteneodeManilaUniversity1

BUILDINGBLOCKSOFNUCLEICACIDS

2

NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

3

NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

4

 NucleusprimarilycontainstheDNA Smallamountsarealsofoundin:

• mitochondriaofeukaryotes• chloroplastsofplants

 PackingofDNA:• 2‐3meterslong• histones

 Gene=DNAsequencetranscribedtoRNA(maycodeforaproteinornot) genome=completecollecDonofhereditaryinformaDonofanorganism

NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

5

NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

6

TYPESOFRNA

•mRNA‐MessengerRNA

•tRNA‐TransferRNA

•rRNA‐RibosomalRNA

•snRNA‐SmallnuclearRNA‐siRNA,miRNA,shRNA

2002Breakthroughoftheyear(RNAi)

NucleicAcidsarelinearpolymers.

7

Eachmonomerconsistsof:

1.asugar

2.aphosphate

Thesugarcomponentsofnucleicacidsaredifferent.RiboseisusedforRNA,DeoxyriboseisusedorDNA.

8

WHICHISMORESTABLE?

Thenitrogenousbasescaneitherbeapurineorpyrimidine.

9

Thenitrogenousbasescaneitherbeapurineorpyrimidine.

10

ThesebaseshaveimportantcharacterisDcs

11

1. keto–enoltautomerism

2. strongUVabsorbance

12ThebaseSUBSTITUTEDfor1’‐OHgroupofthesugar

Thelinkingofasugarandanitrogenousbaseiscalledanucleoside.

SubsDtuDngaphosphatetothe5’‐OHofthenucleosidecreatesnucleoDdes.

13

PHOSPHATE

SUGAR

NITROGENOUSBASE

SubsDtuDngaphosphatetothe5’‐OHofthenucleosidecreatesnucleoDdes.

14

Morethanonephosphatemaybeadachedtothe5’‐OHgroup

15

NucleoDdesareconnectedviathe3’‐OHofonenucleoDdetothephosphateatthe5’posiDonofanothernucleoDde

16

WHICHISMORESTABLE?

17

AshorthandnotaDonmaybeusedtodrawthenucleicacidsequence.Basesequencesarealsousedandwridenfrom5’to3’

18

RECAP:1. DNAandRNAdiffersonthesugarused2. Thenitrogenousbasescanbepurine‐orpyrimidine‐based.

3. Nucleicacidshaveanacidpartandbasicparts‐  AtphysiologicalpH,phosphoricacidlosesitsprotons,therefore(–)charged

‐  Basesarenotyetprotonated,neutral4. Somepartsofthenucleicacidiscapableofhydrogenbonding

3DSTRUCTUREOFDNA

20

Thereareseverallevelsofstructure:

21

1. PrimaryStructure–sequenceororderofthemonomers(inthiscase,thenucleoDdes)

2. SecondaryStructure–Localizedregionsoftheprimarysequencefoldedintoaregular,repeaDngstructuralelement

3. TerNaryStructure–InteracDngsecondarystructurestoformmoreintricate3Dshapes

4. QuaternaryStructure–associaDonofoneormorechainstoformacomplex

Theroadtodiscoveryofthe3DstructureofDNA:

22

MauriceWilkinsandRosalindFranklinnotedtherepeaDngstructuralunitfrompadernsderivedX‐raycrystallography.

LevineanalyzedDNAandascertainedthatitcontainsA,T,C,G.ChargraffrevealedthattheraDobetweenA:TandG:Cis1,possibilityofbasepairing.

RecogniDonthatthebasesareinketo‐form=hydrogenbondingispossible!

Theroadtodiscoveryofthe3DstructureofDNA:

23

WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoNdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

Theroadtodiscoveryofthe3DstructureofDNA:

24

WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoNdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

Theroadtodiscoveryofthe3DstructureofDNA:

25

Majorandminorgroovesarelinedwithsequence‐specificH‐bonding.

Theroadtodiscoveryofthe3DstructureofDNA:

26

WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoDdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecNon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

Theroadtodiscoveryofthe3DstructureofDNA:

27

WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoDdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

Theroadtodiscoveryofthe3DstructureofDNA:

28

WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoDdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracNons

Theroadtodiscoveryofthe3DstructureofDNA:

29

TheDNAcanalsohavemanydoublehelicalforms

30A‐DNA B‐DNA Z‐DNA

TheDNAcanalsohavemanydoublehelicalforms

31A‐DNA B‐DNA Z‐DNA

 A‐DNA:right‐handed,shortandbroad,2.3A,11bpperturn

 B‐DNA:right‐handed,longer,thinner,3.32A,10bpperturn

 Z‐DNA:lem‐handed,longest,thinnest,3.8A,12bpperturn

PhysicalproperDesofDNAdetermineit’sabilitybiologicalacDvity

32

DNAstrandsarecomplimentary–canserveastemplateofeachotherorsomethingelse…(informaDontransferandreplicaDon!)

Butbeforethat,H‐bondsmustbebroken!

ISTHISCHEMICALLYPOSSIBLEorLOGICAL?

Yes,itispossible!

33

DenaturaNon–heaDngofDNAtodisruptH‐bondsandseparatethestrands.Ataround85‐90°CcalledthemelDngtemperature(Tm).

Annealing–gradualcoolingofdenaturedDNAtoassociatethetwostrands

WecanmonitorDNAdenaturaDonusingUV‐Visbecauseofhyperchromiceffect.

34

Hyperchromiceffect–increaseofUVabsorbancewhenDNAisdenaturedduetoalteraDoninthearrangementoftheπelectronsinthearomaDcringsofthebases

DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

35

relaxedDNA

supercoiledDNA

DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

36

DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

37EnzymescalledTopoisomerasescreateorrelaxsupercoils

DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

38

EnzymescalledTopoisomerasescreateorrelaxsupercoils

DNAinlivingorganismscanhavedifferentpossibleterDarystructures.Theymayalsooccurasquadruplexes

39

DNAinlivingorganismscanhavedifferentpossibleterDarystructures.Inhumans,theyarepackedaschromosomes

40

3DSTRUCTUREOFRNA

41

StructuraldifferencebetweenRNAandDNA:

42

1. Sugar(Ribosevs.Deoxyribose)

2.  Uracilvs.Thymine

STERICCLASHES???

StructuraldifferencebetweenRNAandDNA:

43

1.  Sugar(Ribosevs.Deoxyribose)

2. Uracilvs.Thymine

SinglestrandedRNAscanfoldintoloops,helicesorhairpinturns:

44

GeneDcinformaDonfromDNAiscarriedbymessengerRNA(mRNA)totheribosomeforproteinsynthesis.

45

AminoacidforproteinsarecarriedbytRNAsthatcontainmodifiednitrogenousbases

46

Containsmodifiedbases

m1G=methylguanosinem2G=dimethylguanosineI=inosinem1I=methylinosineD=dihydrouridineΨ=pseudouridine

RibosomalRNA(rRNA)containsstructuralfeaturessimilartotRNA

47

SmallnuclearRNA(snRNA)helpsinmRNAprocessinginsidethenucleus(splicing,etc.).Theyareonlyfoundineukaryotes

48

NUCLEICACIDCLEAVINGANDOTHERFORMSOFNUCLEICACIDS

49

Nucleicacidscanbecleavedbyenzymescallednucleases.

50

RestricNonenzymes(aspecificendonuclease)mayalsobeusedtocleavecircularDNAfrombacteria..

51

Nucleicacidsformmanycomplexeswithproteins:virus,chromosomes,snRNP,Ribosomes,Ribonucleoproteinenzymes.

52

OTHERINTERESTINGFACTS

53

BOX10‐1containsinformaDonaboutpurinesandpyrimidines

54

BOX10‐2talksaboutspecialRNAsesthatarebeingtestedasanD‐canceragents

55