Unconventional DNA architecture in a dopamine–bound aptamer complex

Abstract

Aptamers are oligonucleotides that have been selected to bind a particular target. Despite the growing popularity of functional DNA aptamers, there remains limited knowledge of their binding mechanisms, as few have been characterized at the atomic level. Here, we use NMR spectroscopy to obtain structural details of RKEC1, a shortened version of a DNA aptamer previously reported to bind dopamine. We find that RKEC1 forms a compact structure upon ligand binding that lacks any Watson-Crick duplex regions or G-quadruplex core, in stark contrast to nearly all predicted and observed DNA aptamer folds. The atomic details explain dopamine specificity amongst structurally similar compounds, and the determined DNA fold was used to guide biosensor design. The aptamer structure further suggests that DNA folding can access an extensive conformational landscape reminiscent of RNA, thus expanding the diversity traditionally captured by predictive algorithms.