We report the first in vitro selection of DNA nanostructures that switch their conformation when triggered by change in pH. Previously, most pH‐active nanostructures were designed using known pH‐active motifs, such as the i‐motif or the triplex structure. In contrast, we performed de novo selections starting from a random library and generated nanostructures that can sequester and release Mipomersen, a clinically approved antisense DNA drug, in response to pH change. We demonstrate extraordinary pH‐selectivity, releasing up to 714‐fold more Mipomersen at pH 5.2 compared to pH 7.5. Interestingly, none of our nanostructures showed significant sequence similarity to known pH‐sensitive motifs, suggesting that they may operate via novel structure‐switching mechanisms. We believe our selection scheme is general and could be adopted for generating DNA nanostructures for many applications including drug delivery, sensors and pH‐active surfaces.