Selection of DNA Aptamers for Root Exudate L-Serine Using Multiple Selection Strategies

Agricultural biosensing can aid decisions about crop health and maintenance, because crops release root exudates that can inform about their status. L-Serine has been found to be indicative of nitrogen uptake in wheat and canola. The development of a biosensor for L-serine could allow farmers to monitor crop nutrient demands more precisely. The development of robust L-serine-binding DNA aptamers is described. Because small molecules can be challenging targets for Systematic Evolution of Ligands by EXponential enrichment (SELEX), three separate DNA libraries were used for SELEX experiments. A L-homocysteine aptamer was randomized to create a starting library for a L-serine selection (randomized SELEX). The final selection rounds of the L-homocysteine selection were also used as a starting library for L-serine (redirected SELEX). Finally, an original DNA library was used (original SELEX). All three SELEX experiments produced L-serine-binding aptamers with micromolar affinity, with Red.1 aptamer having a K-d of 7.9 +/- 3.6 mu M. Truncation improved the binding affinity to 5.2 +/- 2.7 mu M, and from this sequence, a Spiegelmer with improved nuclease resistance was created with a K-d of 2.0 +/- 0.8 mu M. This L-serine-binding Spiegelmer has the affinity and stability to be incorporated into aptamer-based biosensors for agricultural applications.