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Aptamer-aptamer pair and aptamer-antibody pair development

Finding the right affinity ligand pair is a bottleneck in immunoassay development where the Optimer platform can help.

Whether you need an additional reagent to form an aptamer-antibody pair or a complete new aptamer-aptamer pair, we can configure the Optimer discovery process to support you.

Standard proteins and affinity ligands form the critical reagents for IVD assays such as ELISA and lateral flow assays, but discovering affinity ligands that work well as pairs can be challenging.

The antibody pair problem

While you may already have a commercial antibody that works for your protein target, this may not perform well as part of a matched pair. This is especially true for novel biomarkers or less popular biomarkers where the range of well-performing commercial antibodies is limited.

Epitope dominance of many antigens means antibody pair screening fails due to steric hindrance from multiple antibodies targeted to the same site.

Most antigens present epitope dominance, where some of the epitopes are more immunogenic or are simpler to develop antibodies against, leaving other epitopes to which fewer functional antibodies are available.

When screening for antibodies to such antigens, many of the available clones on the market are targeted to the same epitopes or epitopes that are very close together. For antibody pair development this presents issues of steric hindrance. The binding of one antibody leaves no space for the second antibody to bind, effectively blocking their function as a matched pair for your protein.

This is just one of the reasons many antibody pairs do not work.

Both sourcing commercially available antibody pairs and creating custom antibody pairs are risky. Extensive time and cost can be expended to purchase and validate antibodies for pairing, with no guarantee they will work in your end application.

Conventional monoclonal technologies are not optimized for generating antibody pairs and suffer from the immunodominance described above. This means that beyond trying to pair commercially available antibodies, custom antibody generation is also risky.

The Optimer solution

The best chance of getting affinity ligand pairs is to target the development process to generate pairs. This requires an understanding of the target and selection of the best discovery strategy to support success.

The Optimer platform offers increased success in the generation of aptamer pairs compared to antibodies. Optimer binders are optimized aptamers, DNA or RNA ligands that act as an antibody alternative for use in the same assays and applications as antibodies, including the development of aptamer-aptamer pairs or aptamer-antibody pairs.

As the Optimer discovery process is performed entirely in vitro, it removes the reliance on the immune system of antibody-based systems. In vitro discovery allows us to engineer the process to remove epitope-dominance constraints. As described, one of the major problems in finding antibody pairs is finding a good second antibody that reacts with the antigen with high affinity and at a distant enough epitope to the first binder to prevent steric hindrance in binding.

Aptamer as smaller binders with in vitro discovery overcome reliance on the immune system, to deliver increased chance of functional aptamer pairs

Optimer discovery processes overcome epitope dominance through multiple strategies allowing development of high performing aptamer pairs.

Using the Optimer platform there are multiple discovery strategies that can be used both in parallel and sequentially to support aptamer pair development.

Optimer discovery strategies for pair development can involve NGS screening of discovery results to allow identification of different aptamers that could form pairs and the validation of such pairs through downstream assays. This delivers fast results with discovery processes taking as little as 4 weeks.

The second strategy we can employ is the use of the first antibody or aptamer bound to the protein antigen as a target for further discovery efforts. In this way the dominance of the initial epitope is blocked by the antibody/aptamer. Using the bound protein antigen as target material in discovery ensures that the second aptamer binds to a site distant enough from the first to deliver a working aptamer-aptamer pair or aptamer-antibody pair.

Also, as Optimer binders are smaller in size (typically just one tenth the size of antibodies) there is more space around each epitope to reduce steric hindrance.

All aptamer-aptamer pairs and aptamer-antibody pairs we develop are further validated for performance in downstream assays that can be tailored to your specific application to make sure that the ligands you receive in your lab are functional.

Optimer-Optimer pair for SARS-CoV-2

Optimer discovery was performed to the SARS-CoV-2 Spike protein with identification of multiple ligands. Further validation of various pairs via sandwich ELISA showed that optimal performance was obtained using the S1 Optimer as a capture reagent and S2 Optimer 1 as a detection reagent.

Optimer-Optimer pair for a receptor type protein tyrosine phosphatase

Optimer discovery was performed to a receptor type protein tyrosine phosphastase with identification of multiple potential ligands. Further validation via biolayer interferometry showed that the optimal performance was obtained using the capture Optimer and Optimer1 for detection.


Starting Optimer discovery from large libraries of 1014 different aptamer sequences, and incorporating both end assay matrix and counter-targets enables us to remove any aptamers that would not perform with the desired high target affinity and specificity in your assay. Traditionally tricky situations, such as aptamer-aptamer pairs, aptamer-antibody pairs or post-translational modification changes can be easily overcome through the careful tuning of our Optimer platform discovery to your needs.

If you work with immunoassays that rely on antibody pairs and need better performance or new ligands get in touch to see how we can work together to improve your assays.


antibody pairAptamer pairELISALateral FlowLFDproximity extension assays

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