2.1 Structures of Components
Nucleic acids are very long, thread-like polymers, made up of a linear array of monomers callednucleotides.
Different nucleic acids can have from around 80 nucleotides, as in tRNA, to over 10^8 nucleotide pairs in a
single eukaryotic chromosome. The unit of size of a nucleic acid is the base pair (for double-stranded
species) or base (for single-stranded species). The abbreviation* bp is generally used, as are the larger units
Mbp (million base pairs) and kbp (thousand base pairs). The chromosome in Escherichia colihas 4 106
base pairs, 4 Mbp, which gives it a molecular mass of 3 109 Da and a length of 1.5 mm. The size of the fruit
fly genome (haploid) is 180 Mbp which, shared between four chromosomes, gives a total length of 5 6mm.
The genomic DNA of a single human cell has 3900 Mbp and is 990 mm long. How are these extraordinar-
ily long molecules constructed?
2.1.1 Nucleosides and Nucleotides
Nucleotides are the phosphate esters of nucleosides and these are components of both ribonucleic acid
(RNA) and deoxyribonucleic acid (DNA). RNA is made up of ribonucleotides whereas the monomers of
DNA are 2-deoxyribonucleotides.
All nucleotides are constructed from three components: a nitrogen heterocyclic base, a pentose sugar
and a phosphateresidue. The major bases are monocyclic pyrimidinesor bicyclic purines, some species
of tRNA have tricyclic minor bases such as the Wye (Figure 3.17). The major purines are adenine (A)and
guanine (G)and are found in both DNA and RNA. The major pyrimidines are cytosine (C), thymine (T)
and uracil (U)(Figure 2.1).
In nucleosides, the purine or pyrimidine base is joined from a ring nitrogen to carbon-1 of a pentose
sugar. In RNA, the pentose is D-ribosewhich is locked into a five-membered furanosering by the bond
from C-1 of the sugar to N-1 of C or U or to N-9 of A or G. This bond is on the same side of the sugar ring
as the C-5 hydroxymethyl group and is defined as a -glycosylic linkage (Figure 2.2).
In DNA, the pentose is 2-deoxy-D-ribose and the four nucleosides are deoxyadenosine, deoxyguano-
sine, deoxycytidineand deoxythymidine(Figure 2.3). In DNA, the methylated pyrimidine base thymine
takes the place of uracil in RNA, and its nucleoside with deoxyribose is still commonly called thymidine.
However, since the discovery of ribothymidineas a regular component of tRNA species, it has been
preferable to use the name deoxythymidine rather than thymidine. Unless indicated otherwise, it is assumed
that nucleosides, nucleotides and oligonucleotides are derived from D-pentofuranose sugars.
The phosphate esters of nucleosides are nucleotides, and the simplest of them have one of the hydroxyl
groups of the pentose esterified by a single phosphate monoester function. Adenosine 5-phosphate is a
5 -ribonucleotide, also called adenylic acid and abbreviated to AMP (Figure 2.4). Similarly, deoxycytidine
3 -phosphate is a 3 -deoxyribonucleotide, identified as 3-dCMP. Nucleotides containing two phosphate
14 Chapter 2
Figure 2.1 Structures of the five major purine and pyrimidine bases of nucleic acids in their dominant tautomeric
forms and with the IUPAC numbering systems for purines and pyrimidines
*A useful source for IUPAC nomenclature of nucleic acids can be found at http://www.chem.qmul.ac.uk/iupac/misc/naabb.html
and for polynucleotide conformation at http://www.chem.qmul.ac.uk/iupac/misc/pnuc2.html#300.