The structure of DNA

  • Created by: Jenny Le
  • Created on: 14-04-14 14:55


Miescher (1869) - extracted nuclein from human pus cell nuclei, contains P, protease resistant

Kossel and Neumann (1894) - initial identification of the bases in DNA

Hammersten (1900) - DNA contains a pentose sugar

Levene (1929) - the pentose sugar is 2'deoxyribose

Todd and Levene (1920's) - determined the chemical nature of nucleic acids. Repeating units: nucleotides. Two forms: DNA and RNA.

Todd (1930's) - nucleotide linkages

Caspersson (1934) - DNA is a linear macromolecule

Chargaff (1950's) - constancy in base ratios from different species, A=T and G=C

Franklin and Wilkins (1952) - X-ray studies, DNA is helix and gave measurements for the helix

Watson and Crick (1953) - developed Franklin and Wilkins model - double helix

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Nucleotide Building Blocks - Bases


  • nitrogenous 
  • planar molecules
  • two sorts; Pyrimidine & Purine

Purines are two ring bases.

  • Adenine
  • Guanine

Pyrimidines are one ring bases.

  • Cytosine
  • Thymine
  • Uracil
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Nucleotide Building Blocks - Sugar


  • Pentose sugar
    • RNA = ribose
    • DNA = deoxyribose
    • (-OH vs. -H at 2'C)
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Nucleotides and Nucleosides

Difference between nucleotide and nucleoside:

A nucleotide is a phosphorylated nucleoside.

Sugar + base = nucleoside

Sugar + base + P = nucleotide

In AMP and ATP, both nucleotide, the phosphate group(s) is bonded to the sugar at 5'C by an ester linkage.

Synthesis of DNA requires the triphosphate form.

  • PPi is lost in the reaction
  • Nucleotides are joined together to form a polynucleotide
  • Join via P-sugar-P-sugar

Hence:- phosphodiester bond, sugar phosphate backbone, 3' and 5' ends.

Add dNTP ==> PPi released and base addedd 5' to 3' direction

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  • single stranded molecule
  • ribose sugar
  • P groups
  • bases (purines/pyrimidines)
  • phosphodiester links
  • 5' ==> 3'


  • double stranded molecule - two complementary anti-parallel strands with sugar-P backbone and protruding bases.
  • deoxyribose sugar
  • P groups 
  • bases (purines/pyrimidines)
  • hydrogen bonds
  • 5' ==> 3' for each strand
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DNA as genetic material

Most DNA exists as a right handed double helix as predicted by the X-ray crystallgraphy of Wilkins and Franklin. 

It is the B-form found in living cells, other forms can be generated in vitro.

Stable structure:

  • Base stacking/secondary structure and packaging.


  • Copy strands using complementary base pairs as the template

Information Store:

  • Uses the sequence of bases as the code. Reads bases in groups of three, 5' to 3'. Gives mechanism for mutations.

Transfer of information:

  • RNA copy, U not T. Transcription transfers information
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DNA - Linear or Circular?

Eukaryotic nuclear chromosomes - linear dsDNA, extremely long - H. sapiens, 46 chromosomes, 6.6 x 10^9 bp.

Eukaryotic organelle (mitochondron, chloroplast) - circular dsDNA, intermediate length - H. sapiens mitochondria, 16569 bp.

Bacterial genome - circular dsDNA, extremely long - E.coli, 4.6 x 10^6 bp.

Plasmids - circular dsDNA, relatively short - 2.6 x 10^3 bp.

Viruses - linear dsDNA or circular ssDNA, also RNA genome viruses. 

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Heating DNA

When DNA is heated, the double stranded molecule becomes single stranded DNA as the hydrogen bonds break between the base pairs. 

DNA denaturation:

Base pairs separate A=T first, followed by G=C 

Tm: melting temperature, increases with higher GC content.

The reaction is followed by measuring the absorbance at 260nm as ssDNA absorbs more light than dsDNA. 

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Cooling DNA

When ssDNA is cooled, the strands will reanneal

  • due to complementary base pairing.

This does not have to be the original DNA strand it was separated from during heating, also referred to as hybridisation

  • add another ssDNA (or RNA) to the reaction.
  • DNA/DNA (RNA:DNA) hybrids formed 
  • relies on the sequences being complementary
  • a sequence of DNA (or RNA) will form complementary base pairs with ANY likely sequence generating stem loop structures, hairpin loops giving secondary structures seen in many RNA molecules e.g. tRNA.
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Determining GC content

Determination of GC content of a DNA molecule by...

  • Tm
  • Buoyant Density.

Buoyant Density:

  • a linear function of GC content
  • can be used to purify DNA
    • 8M CsCl has about the same density as DNA 
    • Mix with the DNA sample of interest
    • Centrifuge FAST (125 x g, 125 hours)
    • Set up a density gradient in the centrifuge tube, the DNA will form a band at the point where its density is the same as CsCl.
    • Protein will be found at the top of the gradient, RNA will pellet at the bottom of the tube
    • This process can also be used to purify one DNA sample from another, for example plasmid DNA and bacterial cell genomic DNA will form separate bands.
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