DNA Structure

DNA is a polymer with a Sugar-Phosphate repeating backbone. Each sugar has a nitrogenous organic base attached (either Adenine, Thymine, Cytosine or Guanine).

Two Deoxyribose Sugars attached by Phosphate Group - DNA Backbone

DNA backbone. You’ve got a deoxyribose sugar attached to a phosphate group & your sugar attached to a base via a BETA-glycosidic bond (eg forms via condensation reaction). Next to look at the bases!

There are two types of bases – Pyrimidine and Purine. Purines are BIGGER with 2 rings (imagine the bigger work being a smaller molecule).

– Pyrimidines (single ring) – T and C & Purines (double ring) – A & G

  • A and T form 2 hydrogen bonds while C and G form 3.
  • The number of H bonds is important as this will determine the strength of the DNA. DNA with a high CG content will have a higher decomposition temperature than DNA with a high AT content because it has a larger number of H bonds. These H bonds hold the helix together better, requiring more energy to break the helix apart.

A little terminology:

Sugar + Base = Nucleoside

Nucleoside + Phosphate = Nucleotide

A deoxynucleoside is a deoxysugar + base.

An oglionucleotide is a polymer of repeating nucleotides in a chain with less than 20 repeat units.

A polynucleotide is a longer chain of repeating units.

– Structure of a DNA Helix

  • Bases are hydrophobic and stack on top of each other in the helix.
  • Phosphates are on the outside – so the helix is highly -vely charged.
  • DNA helix has 2 strands – these run ANTI-PARALLEL. Eg.
    5′—————>3′
    3′<—————5′
  • It’s a right handed helix. Imagine a screw – spirals look like they are going down clockwise.

  • Remember that direction! I’ve drawn an extra white arrow going up on the second picture to show what the 5′—->3′ does.

  • This is also known as B-DNA.

– Other (more rare) helix structures

  • A-DNA. Helix follows same direction but the bases are pulled away from the centre of the helix nearer to the backbone. This happens when the DNA is dehydrated.
  • Z-DNA. A normal helix…but backwards! The DNA strands are wound the opposite way, meaning it appears mirrored to normal B-DNA. This occurs in some GC containing sequences at high salt concentrations.

– Packing down the DNA Helix to more condensed structures (eg. Chromatin)

  • Although the DNA helix is a fairly compact structure, this can be further wound to reduce it’s size. Imagine a helix is like a coil, then winding that coil round and round a roll…this picture borrowed from Wikipedia explains visually.
    (Click picture to enlarge in a new window/tab)
  • Chromatin contains 5 main proteins (H1, H2A, H2B, H3, H4) which are very basic (AKA contain lots of +vely charged amino acids like arginine and lysine) and which interact with the -vely changed DNA (due to the phosphate groups as explained previously).
  • 2x (H2A, H2B, H3) form the round structure you see in the second box of the image above. The DNA helix wraps around this 1.6 times before wrapping round another cylindrical structure.
  • Essentially the DNA is arranged around the histone cores like beads on a string which further packs down to form higher order structures such as chromosomes.