December 2015 Newsletter – Base Pair Values

In this Issue:

– What’s new at Base Pair?
– Venn Multiplex™ SELEX

Base Pair Values Statement

Last month we shared our revised Mission Statement after celebrating the completion of our 3rd year in business. This month, we’d like to take this opportunity to share our Values Statement. This statement reflects our guiding principles which we pledge to our customers:

Values Statement
Base Pair is dedicated to problem-solving and innovation in the nucleic acid aptamer space, helping researchers and commercial entities achieve their goals through the provision of novel molecular tools and analysis techniques. We are also dedicated to generating a high return to our investors, while ensuring that employees are rewarded for driving the company’s success, by providing opportunities to participate in that success. We will always operate with the highest degree of scientific and moral integrity in all aspects of our business.
Innovation drives our scientists to continuously improve the way in which we design aptamer screens. Proprietary, new software algorithms power our ability to identify novel aptamer sequences and structural motifs. New methods developed and optimized over the past year in our laboratory allow us to not only develop aptamers directed against as many as thirty different targets at the same time, but also to design screens that identify aptamers recognizing overlapping sets of targets or that selectively recognize a single target while ignoring others. Finally, our new methods allow us to select for aptamers directed against your target, in the very same type of sample that you would like to use for your eventual assay, avoiding matrix background and non-specific binding problems.

Please join us in celebrating the completion of our third year by letting us know how we can help you – whether you are seeking an affinity agent for an internal research project, designing a diagnostic test or pursuing a new therapeutic agent. We are here to help you succeed. Contact Base Pair

Venn Multiplex™ SELEX

Patented, multiplexed, simultaneous aptamer selection against related targets coupled with deep, next-generation sequencing allows aptamers with unique binding properties to be readily identified via comparative analysis

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.