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

Abstract

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.

NF2 regulates IP3R‐mediated Ca2+ signal and apoptosis in meningiomas

“…MD simulations were performed to further confirm the importance of F1 in the interaction between NF2 and IP3R1‐CTD. Like in our previous studies, 25–27 a computational framework (Figure 4A) involving molecular modeling and docking and MD simulations was utilized to construct a binding model of the NF2 FERM and IP3R1 CTD. In brief, based on the crystal structure of the NF2 FERM (PDB ID: 1H4R 16 ) and the predicted homology model for IP3R1, ZDOCK 17 was used to generate a pool of 10 800 possible docking conformations between NF2 FERM and the IP3R1 CTD.…”