Aptamer Screening Services for Protein and Nucleic Acid Targets

Core Technology: SELEX

The foundation of all these services is the SELEX process, an in vitro method to select aptamers from a vast random library (typically 10^13 – 10^15 unique sequences). The library is incubated with the target, unbound sequences are washed away, and bound sequences are eluted and amplified by PCR (for DNA) or RT-PCR (for RNA). This cycle is repeated 8-15 times to enrich for the tightest binders.

Services for Protein Targets

This is the most common application, as aptamers are often touted as “chemical antibodies.”

1. Standard Protein SELEX:

• Target: Purified, recombinant proteins (e.g., cytokines, receptors, enzymes, viral capsids).

• Key Considerations:

  • Protein Purity & Conformation: Critical for success. Services often require >90% purity and verification of native folding.

  • Immobilization: The protein is usually immobilized on beads (e.g., streptavidin/biotin, Ni-NTA/His-tag) to facilitate partitioning. Some services offer solution-phase SELEX to avoid conformation changes.

  • Counter-Selection: To ensure specificity, libraries are pre-incubated with related proteins or the immobilization matrix to subtract non-specific binders.

2. Specialized SELEX for Complex Proteins:

• Membrane Protein SELEX: For receptors and channels. Requires special handling (e.g., use of nanodiscs, detergent micelles, or whole cells overexpressing the target).

• Post-Translationally Modified Protein SELEX: For targets where phosphorylation, glycosylation, etc., are essential for function.

3. Cell-SELEX (for Cell-Surface Proteins):

• Target: Proteins in their native context on a live cell membrane.

• Process: Uses whole cells (e.g., cancer cells) as the positive target and isogenic control cells (e.g., normal cells) for counter-selection.

• Outcome: Aptamers that recognize specific cell states (e.g., tumor-specific surface markers), often without prior knowledge of the exact protein target.

4. Tissue/In Vivo SELEX:

• The most advanced service. The library is injected into an animal model or applied to a tissue section to select for aptamers that can home to specific tissues in vivo.

Services for Nucleic Acid Targets

This is a niche but powerful application, often for diagnostics and structural biology.

1. DNA/RNA Structure SELEX:

• Target: Specific secondary or tertiary structures of nucleic acids (e.g., G-quadruplexes, hairpins, riboswitches).

• Application: Developing biosensors or tools to probe nucleic acid folding.

2. Nucleic Acid-Protein Complex SELEX:

• Target: A specific complex, like a transcription factor bound to its DNA element.

• Goal: Select aptamers that either disrupt or stabilize the interaction.

3. Hybrid Target SELEX:

• Target: Complexes like chromatin or viral nucleocapsids (protein + nucleic acid).

Typical Service Workflow (What You Can Expect)

1. Consultation & Design: Provider discusses target, desired aptamer properties (Kd, specificity, nuclease resistance for RNA), and application (diagnostic, therapeutic, purification).

2. Library & Selection Strategy: Provider chooses library (DNA, RNA, modified RNA like 2′-F, 2′-OMe) and SELEX method (e.g., Capture-SELEX, Magnetic Bead SELEX, CE-SELEX for higher stringency).

3. The SELEX Process: The provider performs iterative selection rounds, monitoring enrichment via quantitative PCR or sequencing.

4. Next-Generation Sequencing (NGS) & Bioinformatics:

   • NGS: Pools from later rounds are deeply sequenced.

   • Bioinformatics: Clustering analysis identifies enriched sequence families and consensus motifs. This is a major value-add of modern services.

5. Candidate Synthesis & Validation:

   • Top 5-20 candidate sequences are chemically synthesized.

   • Primary Validation: Binding affinity (Kd) measured via techniques like Surface Plasmon Resonance (SPR), Bio-Layer Interferometry (BLI), or Electrophoretic Mobility Shift Assay (EMSA).

   • Secondary Validation: Specificity tests against counter-targets, functional assays (e.g., inhibition of enzyme activity).

6. Deliverables:

   • A final report with sequences, structural predictions, and binding data.

   • Physical aliquots of the validated aptamers.

Key Considerations When Choosing a Provider

• Expertise & Experience: Look for a proven track record with your target class (e.g., membrane proteins, small molecules).

• Technology Platform: Do they offer advanced SELEX variants (CE-SELEX, Toggle-SELEX for cross-species reactivity) for higher success rates?

• Analysis Capabilities: In-house NGS and bioinformatics are essential.

• Validation Assays: Ensure they provide robust, quantitative binding data (SPR/BLI is gold standard).

• Ability to Incorporate Modifications: For therapeutic/diagnostic use, can they select nuclease-resistant RNA analogs (2′-F, 2′-OMe) or introduce specific labels (fluorescent, biotin) during selection?

• Turnaround Time & Cost: Typically ranges from 3 to 9 months and $20,000 to $100,000+, depending on complexity.

Leading Providers & Models

• Full-Service CROs: Companies like Aptamer Sciences, AptaGen, Base Pair Biotechnologies, Aptamer Group offer end-to-end services.

• Academic Core Facilities: Some universities offer fee-for-service SELEX.

• Therapeutic Developers: Companies like SomaLogic (SOMAmer technology) have proprietary platforms but may partner on specific projects.

Applications of the Resulting Aptamers

• Diagnostics: As capture/detection reagents in biosensors (ELONA, lateral flow assays).

• Therapeutics: As antagonists, agonists, or targeted delivery vehicles (though stability and pharmacokinetics require extensive modification).

• Research Tools: For protein detection, imaging, pull-down assays, and modulating protein function.

• Separation & Purification: As affinity ligands in chromatography (aptamer-affinity columns).

In summary, aptamer screening services provide a specialized, outsourced pathway to generate high-quality molecular recognition elements. Success hinges on a clear definition of the target, a well-designed selection strategy, and a provider with the right technological depth to navigate the complexities of the SELEX process.