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

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’

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

Sterically Allowed

Base Orientations Anti or Syn

DNAFORMSBFormDNA-

• Righthanded,majorform,hydrated• MajorGroovewideanddeep,MinorGroove

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

HbondingisrequiredforspecificityofbaseparingbutcontributeslittletostabilityofDNAstructure…whatdoesthatmean?HbondingbetweenbparereplacedbyHbondswithbasesandwaterwhendenatured…sosomethingelsehastoaddtoDNAstructurestability…

AFormDNA-

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

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

• 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