Cross-Binding of Four Adenosine/ATP Aptamers to Caffeine, Theophylline, and Other Methylxanthines

The classical DNA aptamer for adenosine and ATP was selectedtwiceusing ATP as the target in 1995 and 2005, respectively. In 2022, thismotif appeared four more times from selections using adenosine, ATP,theophylline, and caffeine as targets, suggesting that this aptamercan also bind methylxanthines. In this work, using thioflavin T fluorescencespectroscopy, this classical DNA aptamer showed K (d) values for adenosine, theophylline, and caffeine of9.5, 101, and 131 & mu;M, respectively, and similar K (d) values were obtained using isothermal titration calorimetry.Binding to the methylxanthines was also observed for the newly selectedAde1301 aptamer but not for the Ade1304 aptamer. The RNA aptamer forATP also had no binding to the methylxanthines. Molecular dynamicssimulations were performed using the classical DNA and RNA aptamersbased on their NMR structures, and the simulation results were consistentwith the experimental observations, explaining the selectivity profiles.This study suggests that a broader range of target analogues needto be tested for aptamers. For the detection of adenosine and ATP,the Ade1304 aptamer is a better choice due to its better selectivity.