5.2.2 Secondary structure of nucleic acids
The two polynucleotide chains in DNA are usually found in the shape of aright-handed
double helix, in which the bases of the two strands lie in the centre of the molecule, with
the sugar–phosphate backbones on the outside. A crucial feature of this double-
stranded structure is that it depends on the sequence of bases in one strand being
complementary to that in the other. A purine base attached to a sugar residue on one
strand is always hydrogen bonded to a pyrimidine base attached to a sugar residue on
the other strand. Moreover, adenine (A) always pairs with thymine (T) or uracil (U) in
RNA, via two hydrogen bonds, and guanine (G) always pairs with cytosine (C) by three
hydrogen bonds (Fig. 5.4). When these conditions are met a stable double helical
structure results in which the backbones of the two strands are, on average, a constant
distance apart. Thus, if the sequence of one strand is known, that of the other strand can
be deduced. The strands are designated as plus (þ) and minus () and an RNA molecule
complementary to the minus () strand is synthesised during transcription (Section
5.5.3). The base sequence may cause significant local variations in the shape of the DNA
molecule and these variations are vital for specific interactions between the DNA and
various proteins to take place. Although the three-dimensional structure of DNA may
vary it generally adopts a double helical structure termed the B form orB-DNAin vivo.
There are also other forms of right-handed DNA such as A and C, which are formed
when DNA fibres are subjected to different relative humidities (Table 5.1).5 3 3 5 Fig. 5.3The antiparallel nature of DNA. One strand in a double helix runs 5’ to 3’, whilst the other strand runs in
the opposite direction 3’ to 5’. The strands are held together by hydrogen bonds between the bases.141 5.2 Structure of nucleic acids