2.2 Standard DNA Structures
Structural studies on DNA began with the nature of the primary structure of DNA. The classical analysis,
completed in mid twentieth century, is easily taken for granted today when we have machines for DNA
oligomer synthesis that pre-suppose the integrity of the 3-to-5phosphate diester linkage. Nonetheless, the
classical analysis was the essential key that opened the door to later studies on the regular secondary struc-
ture of double-stranded DNA and thereby primed the modern revolution known as molecular biology.
Standard structuresfor DNA have generally been determined on heterogeneous duplex material and are
thus independent of sequence and apply only to Watson–Crick base-pairing.
2.2.1 Primary Structure of DNA
Klein and Thannhauser’s work (Section 1.4) established that the primary structure of DNA has each nucleo-
side joined by a phosphate diester from its 5-hydroxyl group to the 3-hydroxyl group of one neighbour
and by a second phosphate diester from its 3-hydroxyl group to the 5-hydroxyl of its other neighbour.
There are no 5-5or 3-3linkages in the regular DNA primary structure (Figure 2.15). This means that
the uniqueness of a given DNA primary structure resides solely in the sequence of its bases.
2.2.2 Secondary Structure of DNA
In the first phase of investigation of DNA secondary structure, diffraction studies on heterogeneous DNA
fibres identified two distinct conformations for the DNA double helix.^2 At low humidity(and high salt) the
24 Chapter 2
Figure 2.15 The primary structure of DNA (left) and three of the common shorthand notations: ‘Fischer’ (upper
right), linear alphabetic (centre right) and condensed alphabetic (lower right)