New DNA aptamer probes for small molecule targets

Aptamers are single-stranded nucleic acids that are highly useful for designing biosensors. However, a number of aptamers binding to small molecules were reported not to be able to bind their target analytes, such as arsenic, ethanolamine, ampicillin, and some pesticides. Most of the selections were performed using immobilized target molecules and the binding studies often relied on heterogeneous assays or gold nanoparticle based assays. We articulate the importance of homogeneous binding assays. In addition, some new DNA aptamers selected in our lab using immobilized DNA library will be introduced. Many of the classic aptamers bind purine derivatives such as adenosine, ATP, and theophylline, but most of the previous selections were carried out using the target immobilization method. Our lab has revisited some of the same target molecules including theophylline, adenosine and also some new targets such as caffeine and uric acid using the library immobilization method. Interesting new aptamers were obtained showing dissociation constants in the nanomolar to low micromolar range as characterized using isothermal titration calorimetry. Cross-binding of different purines by aptamers was also studied. Given the biological importance of purine derivatives, biosensors were also designed for their detection. In addition, our recent work in the selection of DNA aptamers for some antibiotics such as tetracyclines and chloramphenicol and hormones like estradiol9 will be presented. Comparisons are made to previously reported aptamers and fluorescent biosensing strategies using labeled and label-free methods will be discussed.