Aptamers are ssDNA or RNA that bind specific targets with high affinity and selectivity. Their combination of high affinity and selectivity make them excellent drug candidates or diagnostic agents. Aptamers are isolated using a process referred to as SELEX (Systematic Evolution of Ligands by Exponential enrichment). In this process a nucleic acid library containing a random sequence region is incubated with the target of interest. Sequences with affinity for the target are separated from non-binding sequences using filter, chromatography or panning separations. These binding sequences are collected, amplified and purified, generating a new pool for further rounds of enrichment. A significant fraction of sequences in the pool exhibit affinity for the target after 8-15 rounds of selection. Aptamers have been successfully selected for a wide range of targets including small molecules, peptides, proteins and even entire cells. Unfortunately the process for isolating aptamers remains long and complex. In the previous funding cycle we introduced capillary electrophoresis selections (CE-SELEX) which reduced the time required to isolated aptamers from weeks to days. In the current submission we propose to further leverage the advantages of microfluidic systems to further simplify and speed the process. We will also develop microfluidic protocols for selections that are not easily performed using existing techniques. In particular we propose to: 1) Develop an automated, flow through, microfluidic SELEX device. We will combine a micro-FFE separation with flow through PCR and DNA purification to develop a fully automated microfluidic device. We anticipate that this device will be able to perform a single round of selection in as little as 10 minutes. 2) Develop a CE-SELEX protocol for isolating aptamers with affinity for membrane proteins. To date the vast majority of aptamers have been selected to bind soluble proteins. This is unfortunate since ligands for membrane proteins are much more valuable as drug candidates and diagnostic agents. CE-SELEX is ideally suited to perform selections against membrane proteins constituted in micelles or liposomes. 3) Develop a new protocol for isolating aptamers with catalytic activity. Hundreds of aptamers that catalyze reactions have been isolated. Unfortunately, due to the selection process used for isolating these aptamers, almost all of these nucleic acids directly take part in the reaction, limiting their effectiveness. We propose using techniques developed to detect and study individual enzyme molecules as the basis for a new method that isolates aptamers based directly on their catalytic activity.
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