Aptasensor Development: Elucidation of Critical Parameters for Optimal Aptamer Performance

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Abstract
Aptamers are synthetic oligonucleotides specifically selected to bind a certain target. Thanks to their high affinity and sensitivity, aptamers appear as alternative candidates to antibodies for analytical devices and several assays have been reported. However, and contrary to what happens with DNA probes, the aptamers' ability to bind their targets depends on folding and 3-D structure, which may be affected by the incubation conditions and buffer composition. In this report, a systematic evaluation of the parameters with potential effect on the ELAA (Enzyme Linked Aptamer Assay) performance has been carried out. Additionally, diverse ELAA and mixed ELISA/ELAA formats exploiting the thrombin-binding aptamer have been optimized and their efficiencies compared. ELAA results have been confirmed using nuclear magnetic resonance, electrophoresis, and surface plasmon resonance. Our results indicate that parameters such as immobilization strategy, incubation time/temperature, and buffer composition should be optimized for each aptamer as they affect folding and, thus, binding efficiency. Among the studied assays, the mixed ELISA/ELAA sandwich formats showed the lowest limit of detection observed (<1 nM thrombin), while a competition ELAA appeared as the best assay in terms of high sensitivity (1.8 nM) and short assay time (1 h, 30 min). The elucidation of optimal parameters for assay performance reported here clearly indicates that aptamers are unique structures. Formation of the 3-D structures required for target binding is influenced by variable parameters, and unlike DNA/antibody based assays, there are no general recommendations, with each assay requiring individual optimization of parameters.