Nucleic Acids DNA & RNA Basics Bases

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Nucleic Acids DNA & RNA Basics DNA – Right handed helix made of opposite oriented strands of nucleotides RNA – single strands of nucleotides, often forming helix within the same strand and bound to proteins (diverse set of molecules) Bases Purine and Pyrimadine – bases that make up the “nitrogen bases” of DNA, RNA and nucleotides Exist as tautomers Sugar (ribose) backbone

Transcript of Nucleic Acids DNA & RNA Basics Bases

Page 1: Nucleic Acids DNA & RNA Basics Bases

Nucleic Acids DNA & RNA Basics

DNA – Right handed helix made of opposite oriented strands of nucleotides RNA – single strands of nucleotides, often forming helix within the same strand and bound to proteins (diverse set of molecules)

Bases

Purine and Pyrimadine – bases that make up the “nitrogen bases” of DNA, RNA and nucleotides Exist as tautomers

Sugar (ribose) backbone

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Chemical Structure of Nucleotides

COUNT the atoms on base and ribose. Gives rise to 5’ and 3’ orientation

1) InaDNAduplex,strandsareanti-parallel. 2) Individualstrandsaresynthesizedfromthe5’OHoftheribose

tothefree3’OHattheterminusofthestrand.Thus,DNAsequenceshavedirectionalitygoingfrom5’to3’.

3) Theanti-parallelstrandsaresaidtobecomplimentaryduetothehydrogenbondingoccurringbetweenheterocyclicbasesacrossstrandsofduplex.

4) DNAsequencesarewritten5’to3’ 5) Whenacomplimentarystrandisgivenforthe5’to3’strand,

thisisthereversecomplementasitisthe3’strandsequencerewrittenfrom5’to3’

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REPLICATIONTRANSCRIPTIONANDTRANSLATION

Chapter 24 Structure DNA Structure - Antiparallel - Right or left handed around common axis - Sugar-phosphate backbone exposed to solvent - Bases occupy core of center - Minor and Major grooves (where protein aa side chains will bind

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Sterically Allowed

Base Orientations Anti or Syn

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DNAFORMSBFormDNA-

• Righthanded,majorform,hydrated• MajorGroovewideanddeep,MinorGroove

narrowanddeep• Basesareperpendiculartoaxis• Antiforbothpurineandpyrimidine• 11.6bp/turn• C2’endopucker

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HbondingisrequiredforspecificityofbaseparingbutcontributeslittletostabilityofDNAstructure…whatdoesthatmean?HbondingbetweenbparereplacedbyHbondswithbasesandwaterwhendenatured…sosomethingelsehastoaddtoDNAstructurestability…

AFormDNA-

• Righthanded,minorform,dehydrated• FoundinRNA-DNAinteractionsites• WiderandflatterhelixthanBDNA• MajorGroovenarrowanddeep,MinorGroovewideandshallow• Basesaretilted20otoaxis• Antiforbothpurinesandpyrimadines

ZFormDNA-• Lefthanded,minorform,dehydrated• EvidenceforZDNAisbindingproteins• Foundnearstartofgenes–mayalterproteinbindingtoproteinsfortranscription

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• Foundwithhighalternatingpurine-pyrimidinesequences(dGC),duringnegativesupercoilingandhighsaltorselectcationbinding(reducingelectrostaticrepulsionfromphosgroups.

• Notastablehelix• Flatormissingmajorgroove,narrowanddeepminorgroove• Basesarenearlyflat• Altanti–syn• EndopuckerC2’PyrimidinesC3’Purines• C3’endopucker• ThisisthedoublehelicalformofdoublestrandedRNA

DNAHASLIMITEDFLEXIBILITY

• DNAformstransitionfromoneformtoanotherbasedonconditions(water,ionsorbindingproteins)

• Therearechangeswithineachform(pitchofbasepairs)dependingonsequence

• 6(plusbase)torsionalangleshaverestrictedrotationalfreedom

• AlphaandzetaarerestrictedduetointeractionsbetweenriboseandPgroups.

• Alreadymentionedxsynandanticonformation• MostareinantiexceptZDNA• Rotationwithintheriboseislimitedtoaccommodatephosphaterepulsionandsubstituentsofribose

atoms• TheringcannotremainplanarduetocrowdingandeitherC2orC3willbeoutofplane(withC5)C2ORC3ENDOPUCKER• Ribose2or3rdcarbonwillbeslightlyaboveplainwithC5carbon• Resultsinalargeshiftindistancebetweenphosphategroups• ReviewZDNAandhowbothendopuckerconfirmersexist

DNACANBESUPERCOILEDConsideraclosed,circulardoublestrandedDNA. -twistingonestrand(overorunder)willcausekinksleadingtoa“supercoil”-Thenumberofcoilscannotbealteredwithoutfirstcleavingatleastoneorbothofthestrands


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