Aptamers are nucleic acid molecules that have been developed to mimic the selective and tight binding of other molecules such as antibodies. In order to identify an aptamer that is capable of binding to a target molecule, a process called Selex (systematic evolution of ligands by exponential enrichment) is utilised. The strategy relies upon a combination of a selective binding assay and amplification by PCR. A ‘library’ of short single-stranded DNA oligonucleotides is synthesised in vitro, representing every combination of A, C, G and T at each position in the starting material. It is assumed that within this mixture, at least one oligonucleotide chain will be capable of binding specifically to the required target, such as a protein surface, using hydrogen bonding and van der Waals attractive forces along the nucleic acid chain and backbone.
What feature of a single-stranded nucleic acid chain underlies this approach?
The backbone carries five bonds around which there is potential rotation. In single-stranded molecules, rotation about these bonds is relatively easy and the library of short DNA molecules synthesised in vitro will assume many different conformations.
The DNA oligonucleotide library is mixed with the target, unbound chains are removed and then those that have bound specifically are eluted using agents that disrupt bonding. The eluted DNAs are amplified by PCR and subsequent selection rounds performed if required; thus those oligonucleotides (aptamers) that bind to the target are enriched.
There are a number of advantages in the use of aptamers for targeting specific molecules. Aptamers isolated in this way frequently display high association rates with their targets, with similar affinities to those of monoclonal antibodies. Their small molecular mass means that they can circulate easily throughout the body and, as nucleic acids, they are relatively easy to synthesise and are relatively stable. Finally, aptamers can carry therapeutic agents, radioisotopes and other imaging agents, providing potentially powerful tools for research and therapeutic purposes.