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From aptamer to Optimer™

Why we do this. What the benefit is for you.

Aptamers are increasingly being used across the life sciences in research, diagnostics and therapeutics. We have years of experience in developing aptamers to the most challenging targets for use in a variety of applications. But our standard processes no longer deliver just an aptamer.

Combining an understanding of how our reagents are being employed and what are customers need to advance their assays and platforms, we have improved our development processes to offer next-generation aptamers, Optimers. Read on to find out how these differ and what the benefits could be to your project.

Overview

What is an aptamer?

Aptamers were first identified in 1990, as short synthetic single-stranded nucleic acid sequences that can bind to a diverse range of targets. Variation in the DNA or RNA sequence of the aptamer result in the formation of different secondary structures. These different structures allow for specific binding to targets, from metal ions and proteins to cells and microorganisms.

Why use an aptamer?

Aptamers can be complementary to traditional antibodies in some applications or be used instead of an antibody, and the best reagent to use will depend on the application being considered. Compared to traditional antibodies, aptamers offer some key advantages that make them an important part of the affinity reagent arsenal. These include:

    • increased batch-to-batch consistency
    • low/no immunogenicity
    • long shelf-life
  • simple to modify for enhanced stability or incorporation into assays

Because of these benefits, aptamers have been pursued by researchers from academia and industry for use as therapeutics, drug delivery vehicles, diagnostic reagents, in drug discovery and within functional genomics and biosensing applications.

Novel or difficult targets

Often antibodies cannot be developed to certain targets (for example, is the target itself is toxic or non-immunogenic). In these cases, aptamers can help as they are selected and synthesised entirely in vitro with no reliance on the immune system.

Scalability and batch consistency

Antibodies and protein-based affinity reagents often rely on mammalian cell expression for production. While these systems do offer improved scalability and consistency over traditional in vivo reagent generation, issues remain.

Scalability in such biological systems is non-linear, high cost and requires expert knowledge of these processes. This is often a bottleneck in scaling biologics leading to project delays. Similarly, despite improvements in batch consistency with the use of recombinant proteins, living systems are inherently variable and expression can drift, and batch-to-batch variation and standardisation are ongoing challenges across the industry.

As aptamers are synthetic molecules, scalability is far more consistent and almost a linear process, while batch-to-batch variation in production is minimised.

Size

Compared to antibodies, aptamers are small molecules at typically ~30kDa. This small size offers advantages, such as access to difficult to reach epitopes that antibodies, at 150kDa, are excluded from. Additional benefits of the small size of aptamers include being able to penetrate solid tissues more easily for therapeutic targeting of tumours, or as IHC reagents.

antibody v aptamerAptamers at 5X smaller than a standard antibody, offer a number of benefits.

What is an Optimer?

An Optimer is a next-generation aptamer optimised for your needs.

Following the selection of a specific aptamer through our custom screening process, we generate and validate Optimers.

Our aptamer libraries are composed of sequences 100 nucleotides in length, while Optimers are 20-80% of the size of the parent aptamer. We analyse the aptamer at both a sequence and structural level and test multiple fragments of the parent aptamer in functional binding assays to identify the best performing Optimer.

aptamer to optimer

Optimers are smaller oligonucleotide binders that the parent aptamer than the parent aptamer and are optimised for target, performance in the end-use assay and manufacturability. 

Optimised for target and assay environment

Within our screening processes, we include an initial feasibility study. This offers quick information on the potential success of your target within our screening systems for rapid and low-cost go/no-go decisions.

If the feasibility stage is successful, we incorporate multiple rounds of selection for your target and counter-selection against cross-reactive targets within your buffer or matrix of choice, optimising the selected reagent according for target specificity and performance in your assay environment.

Our experts will discuss your end-use aims and needs before the project begins to agree a work schedule that incorporates clear milestones and follows a data-driven model to ensure the best outcome according to the data generated during selection.

Beyond optimisation within the screening process, the small size of Optimers offers further assay benefits, particularly for therapeutics, IHC or biosensing applications. In therapeutic and IHC applications, the small size allows increased tissue penetration and access to epitopes. In biosensing, the smaller size of Optimers increases the proximity between target capture and the sensor surface for increased sensitivity.

Optimised for affinity, stability, and manufacturability

Trimming the parent aptamer to an Optimer reagent increases the binder’s stability, as there is a reduced number of free groups available to interact with other molecules, and a limited number of conformational shapes that the Optimer can take compared to the parent molecule. The improved structural stability of the Optimer often yields improved binding profiles to increase target affinity.

Target binding is a characteristic of both the on-rate of aptamer-target complex formation and the off-rate of aptamer-target dissociation. While the on-rate is typically driven by the probability of the aptamer colliding with the target molecule, in some assays such as LFDs the target is forced to interact with the immobilized aptamer. If the aptamer is not in the required conformation when the target collides binding will not occur. Trimming an aptamer to an Optimer increases structural stability, partially fixing the conformation of the Optimer to promote an increase in on-rate kinetics, and prevent structural rearrangements to non-binding conformation, decreasing off-rate kinetics. Ultimately this give rise to an increase in target affinity.

The small size of the Optimer in comparison to an aptamer offers reduced manufacturing costs and increased manufacturing speed for improved cost-effectiveness in downstream production.

All our standard processes now deliver Optimer reagents to customers for improved performance and cost-effectiveness. For more information on how your project could benefit from Optimer technology please get in touch.

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