Antibody labelling is readily achieved using commercially available reagents (fluorophores, Quantum dots, gold nanoparticles etc). As these reagents target functional groups on amino acids (hydroxyl, amine, or thiol groups), it is difficult to label the antibody in a reliable, uniform and consistent fashion. Labelling reactions of this nature typically leave a heterogeneous mixture of antibodies, with different numbers of labels at different sites; some of which may be in the active site and hence disrupt antibody function. This heterogeneity undoubtedly leads to batch-to-batch variability issues and potentially inconsistent data.
Aptamers are synthetic, so they are easier to manipulate
As aptamers are composed of synthetic nucleic acids; they are readily prepared by solid phase synthesis. This well understood chemical synthesis approach gives aptamers a considerable advantage as they can be prepared to a significantly higher standard.
Functional groups (such as commercially available fluorophores, nanoparticles etc) or coupling groups (such as amine, thiol or azide groups) can be incorporated at any chosen point during the synthesis process. This gives the advantage that the user can define the exact point of attachment for any functional group(s); meaning that the antigen binding site is NEVER DISRUPTED = 100% functional molecules. This consistency and reliability is essential for many applications; including targeted drug delivery.
Site-specific labelling also means that there is little to no heterogeneity in the resulting labelled aptamer and hence more reliable results from ELISA-like assays, Lateral Flow Devices, Biosensors etc.