What Is a Custom Aptamer—and Why Does It Matter?
Aptamers are single-stranded DNA or RNA oligonucleotides that fold into defined 3D structures to bind targets with high affinity and specificity. Unlike antibodies, aptamers are chemically synthesized, readily engineered with functional handles, and can be optimized for stability and performance in your intended assay or biological matrix.
In practical R&D, "custom aptamer development" is rarely just selection. Many projects fail at the transitions:
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Selection - reproducible synthesis (sequence biases, structure sensitivity, batch consistency)
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Binder - functional reagent (matrix effects, nuclease degradation, weak performance in complex samples)
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Prototype - application format (labeling, immobilization, conjugation, assay translation)
That's why we built a stepwise, service-modular workflow that lets you start where you are and scale to where you need to be.
Great Minds Choose Creative Biolabs
Advanced Protocols and Platforms for Aptamer Development
To mirror the way high-performing assay programs are built, we organize aptamer development protocols by critical decision points.
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Decision Points
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Description
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By Selection Format (SELEX Design)
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Protein/target-based selection workflows
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Whole-cell selection strategies when native conformation matters
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Stringency escalation plans (counter-selection, competitor challenge, off-target depletion)
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By Engineering Pathway
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Stability-first: 2'-F, 2'-NH2, 2'-O-methyl, 3' end protection
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Assay-first: fluorescence/biotin labeling, immobilization-friendly handles
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Function-first: bivalent formats, conjugation-ready designs
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By Validation Stage
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Binding kinetics & specificity confirmation (orthogonal methods where appropriate)
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In vitro stability/cytotoxicity checks to de-risk experimental use
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In vivo analysis planning for research-stage evaluation
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Design Your Workflow
Case Studies
Case 1
Building an ELONA-ready aptamer pair for quantitative detection
A team needs a binder set suitable for a sandwich-style ELONA format. We align SELEX conditions to favor specificity in the target matrix, then carry candidates into optimization, labeling strategy, and ELONA format development (direct vs sandwich, aptamer/antibody combinations), delivering an assay package with recommended controls and data interpretation guidance.
Case 2
Stabilized, functionalized aptamer conjugate for targeted binding studies
For a cell-surface target, the project requires an aptamer that remains stable and performs reliably after conjugation. We combine modification planning (nuclease resistance + functional handle), conjugation execution (e.g., nanoparticle functionalization), and characterization to confirm that performance is retained post-conjugation.
FAQs about Custom Aptamer Development
What information do you need to start a custom aptamer project?
At minimum: target identity and format (purified protein, peptide, cell, complex sample), intended application (binding reagent, ELONA, biosensor, conjugate), desired specificity constraints (off-targets to deplete), and sample matrix considerations. These inputs guide SELEX design and the downstream modification/validation plan.
Can you work with difficult targets like membrane proteins, multi-subunit complexes, or low-abundance proteins?
Yes—these targets are often feasible, but success depends heavily on target presentation and selection design. For membrane proteins, we may recommend cell-based or native-like formats to preserve conformation. For complexes, we can incorporate counter-selection to reduce binders against unwanted components. For low-abundance targets, enrichment strategy and background suppression become central.
Do you offer DNA aptamers, RNA aptamers, or both—and how do we choose?
We support both. The selection depends on your endpoint: RNA aptamers can offer strong structural diversity but often require thoughtful stabilization; DNA aptamers can be simpler to handle and synthesize consistently. If your work involves nuclease-rich environments or extended incubation, chemical modification strategy becomes critical regardless of type. We typically recommend a modality based on matrix exposure, assay design, desired stability, and downstream functionalization needs (labels, linkers, conjugation handles).
Can you develop aptamer conjugates without sacrificing binding affinity?
Yes. This is a common request and we approach it carefully. We evaluate where to attach (terminus vs internal position), which linker chemistry fits your payload and use case, and how to validate post-conjugation binding in a way that reflects your endpoint. In many projects, the key risk is steric hindrance or conformational disruption.
We already have an aptamer sequence. What can you do beyond synthesis?
If you already have a candidate, we can help you turn it into a reliable tool through optimization, modification, conjugation, and characterization. Typical upgrades include truncation to reduce unnecessary regions, redesign to improve robustness, and modification plans to improve nuclease resistance or labeling compatibility.
How do you validate performance for assay development such as ELONA?
For ELONA-oriented development, we prioritize signal-to-background behavior, reproducibility, and specificity in the matrices that matter to you. We help select capture/detection strategies (aptamer–aptamer, aptamer–antibody, or other pairings), define appropriate controls, and tune key parameters like blocking, incubation, and wash conditions.
