Often described as synthetic antibodies, aptamers are single stranded DNA or RNA molecules that fold into defined secondary structures and bind to targets with high affinity and specificity. In 1990, the first aptamer was developed against T4 DNA Polymerase using RNA1. The field of aptamer selection and the use of these aptamers has expanded significantly. Now aptamers are developed using both RNA and DNA, as well as non-natural bases, backbones, and small molecules. Aptamers have been used in a variety of applications; detection molecules in ELISA-like assays, protein-specific tissue staining, targeted drug delivery, and as an FDA-approved treatment for macular degeneration2. Aptamers are developed using a process known as SELEX (Systemic Evolution of Ligands by Exponential Enrichment). During SELEX, trillions of random DNA oligos are mixed with the target molecule; sequences that bind to the target are then collected and amplified. After multiple rounds of selection, the DNA is sequenced and individual sequences are evaluated for binding. Using SELEX aptamers with affinity for a variety of targets can be developed, including proteins, peptides, and small molecules.
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Due to their robust binding affinities for specific biomolecules, aptamers have been explored as an alternative to antibodies. Aptamers offer the following advantages:
RayBiotech uses state of the art techniques in our SELEX process to generate high quality aptamers for our customers. Traditionally, the target must be bound to a solid support, altering the target the aptamer is selected for. However, at RayBiotech we use CE (Capillary Electrophoresis) to separate binding sequences, allowing the DNA to interact with the protein in free solution. While traditional SELEX can require 10 rounds of selection or more, CE is effective enough to identify aptamers in as few as 3 rounds, which helps to reduce the effects of PCR bias on the selection3. The use of CE also allows us to monitor the development of the aptamer library throughout the selection process.
In addition, RayBiotech uses NGS (Next Generation Sequencing) instead of plasmid cloning techniques to identify individual aptamers. We utilize the data gained in NGS to analyze the entire aptamer pool and identify common aptamer sequences, motifs, and other patterns in the library. Using this information allows us to identify better aptamer candidates than those identified by randomly selected clones.
Aptamer development has 3 primary phases: