aptamers for their target molecule is nicely illustrated by one such example that binds with high affinity
(KD0.6 M) to theophylline (1,3-dimethylxanthine) but binds the highly similar structure caffeine (1,3,7-
trimethylxanthine) about 10^4 fold less efficiently.
The selection of an aptamer with high affinity for the blood-clotting protein thrombin was the first
example of a nucleic acid ligand designed to bind to a protein target that does not normally interact with
DNA.^56 Such aptamers show affinities between 25 and 200 nM and contain a highly conserved 14–17 base
consensus sequence. NMR of the 15-mer aptamer d(GGTTGGTGTGGTTGG) and X-ray crystallography
as a complex with thrombin have revealed that the oligonucleotide forms a DNA quadruplex structure
(Sections 2.3.7 and 9.10.2). Such aptamers have potential clinical application as anti-coagulants.^54
5.7.3.3 Selection of Nucleic Acid Catalysts. SELEX has also been exploited to generate nucleic
acid-based catalysts for a wide range of chemical reactions. Examples including RNA cleavage, DNA
cleavage, DNA ligation, DNA phosphorylation, porphyrin metalation, DNA capping, DNA depurination,
amide bond formation and the Diels–Alder reaction and the ability for stereochemical control during
catalysis highlight the potential of SELEX in the area of synthetic organic chemistry.53,57–59Initial selec-
tions require protocols in which the chemical reaction is intramolecular (in cis), for example, self-
cleavage, self-alkylation or self-phosphorylation. However, the analogous intermolecular reaction (in
trans) with a separate substrate molecule is generally of more practical value.
In an example derived from the work of Santoro and Joyce,^60 a DNA catalyst (DNAzyme) capable of
the specific cleavage of an HIV RNA target sequence was identified (Figure 5.27). Here a synthetic DNA
library containing a central randomised region of 50 nucleotides flanked by 5and 3constant sequences
200 Chapter 5
Figure 5.26 The generation of DNA aptamers using SELEX