Because aptamer performance is optimal under selection conditions, we recommend that you consider a custom development project for any specialized assay or use conditions. Base Pair’s custom aptamer discovery and development service is highly customized to meet each customer’s unique needs.  Here is a general overview of our aptamer development process, describing key features of each phase.  As we work with you to understand your project, we will develop and share with you a detailed plan, aligned with your goals and objectives.

Phase 1: Consult

Every Base Pair aptamer discovery project begins with an in-depth customer conversation, to give our scientists a clear understanding of your needs. Such conversations frequently take place under the auspices of a mutual non-disclosure agreement. We are glad to review your institution’s agreement or provide our own.  We can also initiate this conversation without an agreement, if preferred.


Phase 2: Design

  • LIBRARY SELECTION: Base Pair chooses or designs a library of aptamer candidades to use in this project. This library might be one of our DNA or RNA libraries containing ~1015 unique sequences, or may be one of our standard modified DNA libraries, with improved avidity for certain protein-based or relatively hydrophobic targets, plus increased conformational diversity. Alternatively, it may be a highly customized library, with additional functionality, such as particular conformational changes that take place upon binding, uncovering or protection of key sequences, addition of specialized chemistry groups that provide an additional level of target specificity or avidity, etc.
  • SELEX DESIGN: Base Pair designs the selection process, including selection conditions, anticipated number of rounds of SELEX, concentrations of buffers or other solutions used as the selection matrix, immobilization methods and surface if needed, and timing for each step. Negative targets are identified and the rounds in which they will be used are determined.
  • SCREENING ASSAYS & FUNCTIONAL TESTS: Screening assays are designed, leveraging the decades of assay development experience of our scientific team. Functional performance tests to evaluate aptamer function in the end-use application are established.
  • PROJECT PROPOSAL: During this phase, Base Pair will present you with a detailed proposal, which will include our recommended strategy, pricing and projected timelines. Upon agreement, we proceed with the project.

SELEX aptamer selection process

Phase 3: Select

In phase 3, multiple rounds of SELEX are performed, using the strategy chosen in the DESIGN phase.  The aptamer candidate pool is reduced from ~1015 sequences to an enriched pool of  ~106 candidates during this process.  If your project has negative targets, the library is depleted of aptamers that bind those targets prior to and/or during SELEX.

If your project has multiple targets, then in the final round, Base Pair will use its patented Multiplex SELEX DNA barcoding and sequence analysis method to associate individual aptamer candidates with their cognate target(s).  If you are interested in identifying specific- and pan-binders, then Base Pair will use its VENNmultiplexTM SELEX method to analyze the resulting sequences.  At the end of this phase, Base Pair performs next generation sequencing and uses its proprietary bioinformatics methods to choose a subset of the enriched candidate pool to analyze further in the later phases of the project.


Phase 4: Screen

In Phase 4, Base Pair performs one of several types of high throughput screens, including Next Generation Sequencing (NGS), to narrow the pool to a smaller set of the best candidates. Such tests are tailored to your particular project and depend on your target type(s) and your desired end use of the aptamers. Affinity measurements may be made during this phase as well.

Phase 5: Apply

Base Pair will use its technical expertise to perform application-specific tests to identify the best candidates to provide to you for your evaluation. We can design and develop enzyme-linked aptamer sorbent assays, fluorogenic microplate assays, microscopy-based assays, flow cytometry assays, lateral flow assays, redox sensor-based assays and others.

Phase 6: Evaluate

Samples of the final candidates are provided for your evaluation, in a form suited for your application – as unmodified oligonucleotides, with reactive groups for coupling to a label or surface, or as conjugates of fluorescent, quencher or redox labels, enzymes or other proteins, additional sequences, gold particles, polystyrene or magnetic beads, chromatography resins or other molecules, particles or surfaces.

Aptamer modification

Phase 7: Mature

If desired, Base Pair will also perform aptamer maturation studies for you. These studies can include truncation analysis, single or multi-base substitutions, randomization of particular regions of the molecule or modifications to secondary regions that increase or reduce predicted melting temperatures. Sequences can also be modified to protect them from nuclease attack, increase hydrophobicity, or to add new functionality, such as the creation of tandems, sensors, or the like.

We are excited about your interest in aptamers. Please feel free to contact us if you have any questions. We would love to learn more about your current project so that we can design and propose an aptamer-based solution for you.