De Novo Evolution of an Antibody-Mimicking Multivalent Aptamer via a DNA Framework

Multivalent interactions can often endow ligands with more efficient binding performance toward target molecules. Generally speaking, a multivalent aptamer can be constructed via post-assembly based on chemical structural information of target molecules and pre-identified monovalent aptamers derived from traditional systematic evolution of ligands by exponential enrichment (SELEX) technology. However, many target molecules may not have known matched aptamer partners, thus a de novo evolution will be highly desired as an alternative strategy for directed selection of a high-avidity, multivalent aptamer. Here, inspired by the superiority of multivalent interactions between antibodies and antigens, a direct SELEX strategy with a preorganized DNA framework library for an Antibody-mimicking multivalent aptamer (Amap) selection to epithelial cell adhesion molecule (EpCAM), a model target protein is reported. The Amap presents a relatively good binding affinity through both aptamer moieties concurrently binding to EpCAM, which has been confirmed by affinity analysis and molecular modeling. Furthermore, dynamic interactions between Amap and EpCAM are directly visualized by magnetic tweezers at the single-molecule level. A nice binding affinity of Amap to EpCAM-positive cancer cells has also been verified, which hints that their Amap-SELEX strategy has the potential to be a new route for de novo evolution of multivalent aptamers.

Automated summary

Multivalent interactions enhance the binding efficiency of ligands to target molecules. A direct SELEX strategy using a preorganized DNA framework library was developed to select an antibody-mimicking multivalent aptamer (Amap) for epithelial cell adhesion molecule (EpCAM). Amap exhibits good binding affinity through both aptamer moieties binding to EpCAM simultaneously, and this strategy has the potential to be a new route for de novo evolution of multivalent aptamers.