Nucleic Acid Structure

• The protonation state of the bases changes in different pH
• Purines = adenine and guanine
• Purines contain two aromatic rings
• Pyrimidines = cytosine and thymine/uracil
• Pyrimidines contain one aromatic ring
• Thymine has one extra methyl group compared to uracil
• Chargaff purified purines and pyrimidines and compared their ratios in different organisms
• Chargaff determined that adenine base pairs with thymine, and guanine base pairs to cytosine
• adenine base pairs with thymine
• guanine base pairs to cytosine
• Properties of bases

  • O and N are hydrogen bond acceptors
  • NH2 and NH are hydrogen bond donors
• Cytosine and guanine can form three hydrogen bonds
• Adenine and thymine/uracil can form two hydrogen bonds
• 1': N-glycosidic bond attaches here
• 2': OH attaches here for ribose, H attaches here for deoxyribose
• 3': OH group where nucleotides attach
• 5': Phosphate attaches here
• Sugars connect by phosphodiester bonds to create the sugar-phosphate backbone
• Nucleic acids are synthesised 5' to 3'
• N-glycosidic bonds are formed between the base and the sugar
• What interactions form the double helix?

  Hydrogen bonds, ionic interactions, hydrophobic interactions
• Hydrogen bonds between bases
• Guanine and cytosine base pairing is stronger as they contain three hydrogen bonds, whereas adenine and thymine only have two
• Ionic interactions cause the DNA helix to twist as the negative phosphates of the backbone repel against interactions that favour base pairing
• Bases have hydrophobic ring structures
• bases will aggregate together in the middle of the helix due to their hydrophobic ring structure
• The electron clouds of the bases stack at a distance that leads to attractive Van der Waals forces
• Bases absorb at 260nm
• RNA absorbs more at 260nm due to being single-stranded
• Hyperchromic effect

  • Due to base stacking, double-stranded nucleic acid absorbs less at 260nm
• The major and minor grooves are formed on the basis of the angle between N-glycosidic bonds
• The major groove is larger and therefore allows for interactions with proteins
• The major groove has more constituents pointing out, allowing for greater interactions with proteins
• The OH on the 2' position of ribose causes instability in basic environments
• Instability of RNA in basic environments:

  1. The OH loses a H to become O-
  2. O- attacks the slightly positive P in the phosphodiester bond, causing it to break
• Cytosine deamination to uracil occurs spontaneously
• Uracil is recognised and removed from DNA to prevent mutations
• As RNA normally contains uracil, it cannot be recognised for removal if it has occurred due to the deamination of cytosine
• Reasons that RNA is less stable than DNA?

  Instability of the OH group in basic environments and inability to recognise uracil from cytosine deamination