Nucleic Acids DNA & RNA Basics Bases
Transcript of 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
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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