A corresponding V-target lattice structure to enhance selection pressure for aptamer selection

Abstract

Aptamers, synthetic single-stranded oligonucleotide molecules that specifically bind to targets, are obtained through systematic evolution of ligands by exponential enrichment (SELEX). Microfluidic-SELEX (M-SELEX) technology has attracted wide attention due to its advantages of integration and high separation efficiency. However, most of the current M-SELEX technologies mainly exhibit characteristics of high separation efficiency to separate oligonucleotide molecules with strong affinity to targets to improve selection pressure, without considering the binding process of targets and oligonucleotide libraries inside microfluidic chips. In this paper, a corresponding V-target lattice structure was constructed in a microfluidic chip, which could enhance the binding process between targets and oligonucleotide libraries. Computational simulations were used to demonstrate that the structure could enhance the mass transfer process in the channel. And then the hemagglutinin protein of influenza A H5N1 virus (HA-H5N1) was used as the target protein for aptamer selection. After three rounds of positive and negative selection, an aptamer with high affinity and high specificity for HA-H5N1 protein was obtained, and the dissociation constant (K_d) was 6.7 ± 2.8 nM. This work provides a new research idea on how to improve selection pressure in SELEX to obtain aptamers with high affinity and high specificity. The microfluidic chip with the corresponding V-lattice structure, which can enhance mass transfer, can be used to select high affinity and high specificity aptamers and also has the potential to be used in detection, sensing and other fields.