Selection of Highly Specific Aptamers

The development of high-quality affinity reagents, with strict discrimination between the desired target and closely related proteins, represents a major challenge for antibodies; however, this can be built in to aptamer selection. Some targets are especially problematic when small changes such as single amino acid substitutions or post-translational modifications (PTMs). As such, caution is often urged  when using antibodies to detect modified proteins in biological samples.

Careful introduction of these closely related counter-selection targets leads to isolation of a population of aptamers with exquisite discrimination.

Similar processes can be used to isolate a population with broad target recognition. For example, aptamers can be isolated using a family of related proteins. The resulting aptamers should then recognise ‘epitopes’ which are common to all of the targets.

The selected aptamer shows specific binding to the target protein (red) with clear distinction of the counter target (blue) which only differs by two PTMs (citrullination = PTM by deimination of arginine). No binding is seen towards the negative control protein (grey).

The selected aptamer shows specific binding to VEGF-B (grey). Cross selectivity was tested with VEGF-A (orange), VEGF-C (yellow) and VEGF-D (light blue) which all show little to no binding. Negative control (dark blue) also shows no binding.

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