Context: A client came to Base Pair Biotechnologies with a difficult set of closely-related, but molecularly distinct protein targets. Additionally, as in many applications, the client had identified a specific set of undesirable targets (in addition to the sample matrix) that the resulting aptamers definitely needed to disregard.
Experiment: Using Base Pair’s patented approach to multiplexed SELEX, all 4 targets in the sample matrix plus background were addressed in the same aptamer selection under identical conditions. Post sequencing identifiers were then applied to the aptamers to compare results from the multiplex SELEX; the diagram below shows the unique sequences determined by Base Pair’s in-house Ion Torrent™ sequencer.
Results: A number of intersections in the diagram were of potential interest to the customer. One commercially interesting set was that comprising 19 distinct aptamer sequences binding all four related protein targets but not the background targets. Representative aptamers from this set are currently being characterized quantitatively for their binding (Kd) via microscale thermophoresis (MST) and backscattering interferometry (BSI) as well as being independently validated by the customer.
Note also the diagram can display sequences unique for each protein as well, generating multiple target aptamers from the same SELEX. Not only is cost per aptamer reduced but the aptamers have been selected in a highly competitive environment, promoting more specificity and better binding characteristics in a complex matrix environment.
