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Structure of DNA

Table of contents

  1. The components of DNA and a few principles
  2. DNA: some facts
  3. What's in a name

  4. Further information

The components

The deoxyribonucleic acid, DNA, is a long chain of nucleotides ask Dr Chromo! which consist of (figure 1):
  1. Deoxyribose ask Dr Chromo! (a pentose = sugar with 5 carbons)
  2. Phosphoric Acid ask Dr Chromo!
  3. Organic (nitrogenous) bases (Purines ask Dr Chromo! - Adenine and Guanine, or Pyrimidines ask Dr Chromo! -Cytosine and Thymine)

a nucleotide
Figure 1: A nucleotide.

Note: in a nucleotide, the atoms of the organic base are numbered 1, 2, ... and the atoms of the sugar, wether it is a deoxyribose like in DNA or a ribose like in RNA, are numbered 1', 2', 5'. Atoms in the sugar component of a nucleotide provide the link between the base and the phosphate group. The 1' carbon is attached to the 9 nitrogen of a purine, or the 1 nitrogen of a pyrimidine. The OH (hydroxyl) group on the 5' carbon is replaced by a bond to the phosphate group (ester bond).

DNA consists of two associated polynucleotide strands that wind together in a helical fashion. It is often described as a double helix.

Each polynucleotide is a linear polymer in which the monomers ask Dr Chromo! (deoxynucleotides), are linked together by means of phosphodiester bridges , or bonds. These bonds link the 3' carbon in the ribose of one deoxynucleotide to the 5' carbon in the ribose of the adjacent deoxynucleotide. This is illustrated in Figure 2 .

Organic Base Organic Base Organic Base purine deoxyribose deoxyribose deoxyribose pyrimidine acid phosphoric acid phosphoric acid phosphoric
Single Stranded DNA
Figure 2: A segment of a single nucleic acid chain : this is a clickable MAP . On the right, is shown the double helix of DNA which is the normal state of the molecule.


Figure 3: The two sugar backbones are oulined in dark grey
deoxyadenylate (A) is in blue,
deoxythymidylate (T) is in green,
deoxyguanylate (G) is in red,
deoxycytidylate (C) is in orange,


Notice that

  • The sugar / phosphate backbone is on the outside while the organic bases project into the inside of the double helix.

  • The organic bases stack on top of each other in parallel plans.

  • By convention a polynucleotide is read from the 5' end to the 3' end.

  • The orientations of the two strands are antiparallel : their 5' - 3' directions are opposite.

    The two strands are held together by the energy of many hydrogen bonds and hydrophobic interaction. The base pairing is regular and precise.


Figure 4: Base pairing. The hydrogen bonds between the NH (blue) and O (red) are in green.

Naming nucleosides and nucleotides:


Definitions Bases
  Adenine (A) Guanine (G) Cytosine (C) Thymine (T)
The combination of a deoxyribose and a base constitutes a deoxynucleoside . Deoxyadenosine Deoxyguanosine Deoxycytidine Deoxythymidine
The combination of a phosphate, a deoxyribose and a base constitutes a deoxynucleotide. Deoxyadenylate Deoxyguanylate Deoxycytidylate Deoxythymidylate

DNA : some facts...

  1. DNA is a double helix.


  2. The Watson and Crick model of a double helix structure provides an answer to the regularity of the composition in bases and its physiological properties (replication in the cell). It is confirmed by diffraction data. Models using beads are useful to handle the concept.


  3. The base composition is variable, but in all cases the amount of adenine is equal to the amount of thymine (A=T). In the same manner, C=G. Consequently A+C= T+G .


  4. E. coli has a single circular DNA molecule of 3,400,000 base pairs. The total length is 1.4 mm.


  5. In man, the DNA molecule in a diploid cell, if fully extended, would have a total length of 1.7 metres. If you unwrap all the DNA you have in all your cells, you could reach the moon ...6000 times!


  6. In addition to functioning as building blocks of nucleic acids, nucleotides are important because they are used to store and transfer chemical energy (e.g. ATP).



What's in a name

D Deoxyribo : the pentose does not have any oxygen in position 2. Compare a deoxyribose with a ribose .
N Nucleic: these molecules were first found in the nucleus of the cell , before being found in mitochondria, chloroplasts (of plant cells), and in the cytoplasm of prokaryotes.
A Acid: only two of the three acid groups of the phosphoric ask Dr Chromo! acid are used to form the DNA chain. The third one gives the phosphoribo-backbone an acidic property.

And to go further

Some illustrations

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