Selecting phosphorodithioate binding agents (thioaptamers) can only be accomplished using AM's proprietary bead-based technology. AM’s bead-based aptamer discovery process has significant advantages relative to conventional solution-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX) approaches. AM’s approach eliminates the repeated rounds of selection and PCR amplification that are required with SELEX. This eliminates problems associated with PCR bias, which disfavors recovery of the most structurally stable aptamers. Significantly, the bead-based process is compatible with any type of DNA or RNA modification that can be incorporated by chemical synthesis. This includes a wide range of modifications that cannot be incorporated during the PCR steps in SELEX such as the phosphorodithioate backbone modifications used in thioaptamers. AM’s process also allows selection of aptamers containing modifications at any combination of single or multiple positions within the sequence. Such modified aptamers cannot be developed using SELEX.

In the bead-based approach, conventional solid-phase oligonucleotide synthesis is performed on millions of beads carrying a non-cleavable linker. Split-and-pool methods are used to create combinatorial libraries in which each bead carries about 10¹² copies of a single sequence, while the sequence varies between different beads. The oligonucleotides are synthesized with the 3’ end covalently attached to the bead. Primer binding sequences are included at each end to allow sequencing of individual beads. Both base and sugar-phosphate backbone modifications can be included at specified positions. AM has developed a proprietary synthesizer that automates this split-and-pool process, greatly simplifying library synthesis.

Specific binding agents (aptamers) are recovered by incubating these bead libraries with a target of interest and recovering individual beads that preferentially bind the target. This is achieved using one of several highly effective methods. After selection for target binding, the oligonucleotide sequence on each selected bead is read and the resulting sequences are resynthesized with the specific chemical modifications that were used in the starting library. The binding agents are then characterized for binding affinity, specificity, and other properties of interest. Once a preferred binding agent is identified, it can be readily synthesized and purified at large scale.