DNA aptamers for common buffer molecules: possibility of buffer interference in SELEX

During a typical aptamer selection experiment, buffer molecules are used at 10 to 50 mM, whereas target molecules could be used at much lower concentrations even in low µM levels. Therefore, doubts existed regarding the potential enrichment of buffer binding aptamers, particularly for failed selections that cannot validate binding of enriched sequences. In this study, we respectively used two common buffer molecules, Tris and HEPES, as target molecules. While we successfully isolated aptamers for Tris buffer, our attempts to generate aptamers for HEPES buffer failed. Thioflavin T (ThT) fluorescence spectroscopy confirmed the dissociation constant of the Tris buffer aptamer to be 2.9 mM, while isothermal titration calorimitry showed a Kd of 43 µM. NMR spectroscopy also confirmed aptamer binding. Finally, we discussed the implications of this buffer selection work and recommended the use of certain buffers.