Loops, hairpins and flipped bases: a DNA aptamer that discriminates Plasmodium lactate dehydrogenase from the blind watchmaker

Abstract

Little is known about how aptamers achieve their specificities in binding and discriminating between closely related targets. Under the pretext of investigating the potential for aptamers in malaria diagnostics, here we solve the crystal structure of a new DNA aptamer which was selected and evolved to bind specifically to the Plasmodium falciparum lactate dehydrogenase (PfLDH) and not bind to human lactate dehydrogenase. The structure reveals two aptamers bind per Plasmodium lactate dehydrogenase tetramer with opposite apical geometry, whereby each aptamer has a distorted hairpin structure. The aptamer comprises a B-helix stem, an asymmetric internal loop involved in target discrimination and an apical loop involved in binding interactions. Each loop contains a critical flipped base. Isothermal titration calorimetry, surface plasmon resonance and electrophoretic mobility shift assay all provide evidence for binding with a dissociation constant in the range 40-70 …