198 Topics in Current Chemistry Editorial Board: A. de Meijere KN ...

Directional Aspects of Intermolecular Interactions 51
suitable for binding to a nucleic acid. In each case these are protuberances from
a fairly spherical protein that can then interact with one of the grooves of DNA.
Specific interactions of these types allow the protein to regulate gene expression.
The recognition of the bases in DNA by hydrogen bonding to the protein involves
patterns, shown in Fig. 39. Each combination of base pairs in a nucleic
acid – G◊ C, A◊ T, C ◊ G, and T◊ A – can be differentiated in the major groove by a
hydrogen-bond pattern [103]. The recognition is less specific in the minor
groove. The side chains of proteins available for such recognition are arginine
with two hydrogen-bond donor groups in the required orientation, glutamic or
aspartic acid with two hydrogen-bond acceptors, and asparagine and glutamine
which contain one donor and one acceptor.
Many crystal structures that involve protein-nucleic acid interactions have
been published in the scientific literature recently. Some show this recognition
scheme as in a zinc finger protein-nucleic acid complex,illustrated in Fig. 40 [71,
a
b
Fig. 40 a, b. Zinc-finger DNA interactions [72]: a interaction of the zinc finger in Fig. 28 with
the bases of an oligonucleotide (note that the zinc ion is distant from the site of the proteinnucleic
acid interaction, merely serving to define the folded structure of the finger), b the
hydrogen bond pattern involved (see Fig. 22)