I'm interested in modifying a polyacrylamide gel-based immunoassay to use aptamers in place of antibodies. In this assay, the proteins are covalently immobilized within the polyacrylamide gel via benzophenone groups. My idea is to run preliminary experiments with thrombin and the well-studied thrombin aptamers (15-mer and 29-mer). Does anyone know how important protein conformation is for thrombin aptamer binding?
My initial hunch is similar to yours, Jon. I'm thinking it is probably worth running some simple experiments to see if the aptamer will bind with a sufficient affinity.
" ... how important protein conformation is for thrombin aptamer binding?" This question cannot be answered in general. It mainly depends on the conditions used during the panning in the SELEX process. It might be helpful to check the original publications of the respective aptamers.
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