High Affinity Aptamer Development Using NGS
Aptamers are small peptides or nucleic acids thatcan bind with high affinity and specificity to defined targets. Aptamers may be used in many applications such as affinity purification, affinity labeling, structural scaffolds and functional interruption of cellular targets in vitro and in vivo. They are readily synthesized and can be obtained inexpensively at high purity. Aptamers are typically identified from large libraries (100 trillion species) through a process (Systematic Evolution of Ligands by Exponential Enrichment: SELEX) of repeated selection and evolution. While aptamers have many positive attributes, the SELEX method for identification, selection and maturation often employs 10 rounds of selection that is time-consuming, labor intensive, and may bias the aptamers identified. Recently, the application of deep sequencing short read Next Generation Sequencing (NGS) (Zimmerman et al PLOSone 2010, Cho et al PNAS 2010) has been used to rapidly identify aptamers with high affinity from the earliest rounds of selection. This approach may enable rapid, cost-effective, and more representative identification of aptamers from large aptamer libraries.