Other forms of base pairing
Ideally, the base pairing should always be of the Watson–
Crick type, although other types of base pairing are
possible. For individual nucleotide bases (not confined by a
double helix), there are several choices of pairing available.
It is possible to rotate one of the bases and obtain ‘reverse
Watson–Crick’ bonding. Another form of base pairing is
known as Hoogsteen base pairs, but in this conformation
the G.C base pair is stable only under slightly acidic
conditions (pH 4–5), due to the necessary protonation of
cytosine. These are only examples of many alternative
forms of base pairing in DNA; most are rare, but could be
induced by changes in the environment (e.g. low pH), and
the result of the different base pairing would be mutations
in the newly replicated DNA sequence.
The Watson–Crick form of base pairs have the same
width for A.T, T.A, G.C and C.G base pairs, and they all
readily fit within the phosphate backbone of the DNA
double helix. It is worth noting that some DNA repair
enzymes scan the DNA, checking the width of the helix for
any bulges (likely due to purine–purine base pairs) or dips
(perhaps due to pyrimidine–pyrimidine base pairing).
Also, the reverse Watson–Crick and other forms of
alternative base pairing within the context of duplex
DNA is likely to result in a distortion of the helix, which the
repair enzyme might be able to detect