Ding Yuzhe, Xie Yachen, Li Albert Zehan, Huang Po-Jung Jimmy, Liu Juewen
Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
Biochemistry. 2023 Aug 1;62(15):2280-2288. doi: 10.1021/acs.biochem.3c00260. Epub 2023 Jul 11.
The classical DNA aptamer for adenosine and ATP was selected twice using ATP as the target in 1995 and 2005, respectively. In 2022, this motif appeared four more times from selections using adenosine, ATP, theophylline, and caffeine as targets, suggesting that this aptamer can also bind methylxanthines. In this work, using thioflavin T fluorescence spectroscopy, this classical DNA aptamer showed values for adenosine, theophylline, and caffeine of 9.5, 101, and 131 μM, respectively, and similar values were obtained using isothermal titration calorimetry. Binding to the methylxanthines was also observed for the newly selected Ade1301 aptamer but not for the Ade1304 aptamer. The RNA aptamer for ATP also had no binding to the methylxanthines. Molecular dynamics simulations were performed using the classical DNA and RNA aptamers based on their NMR structures, and the simulation results were consistent with the experimental observations, explaining the selectivity profiles. This study suggests that a broader range of target analogues need to be tested for aptamers. For the detection of adenosine and ATP, the Ade1304 aptamer is a better choice due to its better selectivity.
1995年和2005年分别以ATP为靶标两次筛选出经典的腺苷和ATP DNA适配体。2022年，在以腺苷、ATP、茶碱和咖啡因作为靶标的筛选中，该基序又出现了四次，这表明该适配体也能结合甲基黄嘌呤。在本研究中，利用硫黄素T荧光光谱法，该经典DNA适配体对腺苷、茶碱和咖啡因的解离常数分别为9.5、101和131 μM，采用等温滴定量热法也得到了类似的解离常数。新筛选出的Ade1301适配体也观察到与甲基黄嘌呤的结合，但Ade1304适配体未观察到。ATP的RNA适配体也不与甲基黄嘌呤结合。基于经典DNA和RNA适配体的核磁共振结构进行了分子动力学模拟，模拟结果与实验观察一致，解释了选择性概况。本研究表明，需要对更多种类的靶标类似物进行适配体测试。对于腺苷和ATP的检测，Ade1304适配体因其更好的选择性是更好的选择。
